Query 029591
Match_columns 191
No_of_seqs 149 out of 530
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 15:22:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029591.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029591hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00062 TATA-box-binding prot 100.0 2.3E-68 5E-73 434.8 24.0 179 13-191 1-179 (179)
2 cd04516 TBP_eukaryotes eukaryo 100.0 1.5E-67 3.3E-72 428.5 23.6 174 13-186 1-174 (174)
3 COG2101 SPT15 TATA-box binding 100.0 3.9E-66 8.5E-71 414.5 20.8 179 10-188 4-184 (185)
4 KOG3302 TATA-box binding prote 100.0 5.8E-66 1.3E-70 419.4 21.6 182 10-191 19-200 (200)
5 PRK00394 transcription factor; 100.0 1.8E-64 3.8E-69 412.2 23.8 175 14-188 1-177 (179)
6 cd00652 TBP_TLF TATA box bindi 100.0 1.6E-64 3.5E-69 410.9 23.4 173 13-185 1-174 (174)
7 cd04518 TBP_archaea archaeal T 100.0 2.6E-64 5.7E-69 409.5 23.6 173 13-186 1-174 (174)
8 cd04517 TLF TBP-like factors ( 100.0 9.1E-64 2E-68 406.4 23.6 173 12-185 1-174 (174)
9 PF00352 TBP: Transcription fa 100.0 2.5E-31 5.4E-36 193.1 10.8 86 101-187 1-86 (86)
10 PF00352 TBP: Transcription fa 100.0 5.8E-31 1.3E-35 191.1 12.0 84 13-96 3-86 (86)
11 COG2101 SPT15 TATA-box binding 100.0 4.2E-29 9.2E-34 200.8 10.9 87 11-97 96-184 (185)
12 PRK00394 transcription factor; 100.0 2.4E-28 5.1E-33 199.6 12.2 87 11-97 89-177 (179)
13 cd04518 TBP_archaea archaeal T 100.0 5.1E-28 1.1E-32 196.8 11.9 85 11-95 90-174 (174)
14 cd04516 TBP_eukaryotes eukaryo 99.9 1.4E-26 3E-31 188.4 11.1 83 104-187 2-84 (174)
15 PLN00062 TATA-box-binding prot 99.9 2.3E-26 4.9E-31 187.8 11.1 83 104-187 2-84 (179)
16 cd00652 TBP_TLF TATA box bindi 99.9 4.2E-26 9.1E-31 185.5 11.6 85 10-94 89-174 (174)
17 cd04517 TLF TBP-like factors ( 99.9 7.3E-25 1.6E-29 178.3 11.2 83 103-187 2-84 (174)
18 KOG3302 TATA-box binding prote 99.8 1.4E-20 3.1E-25 153.8 10.2 86 12-97 111-197 (200)
19 PF11858 DUF3378: Domain of un 96.8 0.0018 3.9E-08 46.6 3.8 32 47-78 27-58 (81)
20 COG4871 Uncharacterized protei 96.6 0.017 3.7E-07 46.9 8.6 63 30-95 47-109 (193)
21 PF11858 DUF3378: Domain of un 95.8 0.012 2.6E-07 42.4 3.4 36 138-173 27-62 (81)
22 TIGR00716 rnhC ribonuclease HI 93.9 0.12 2.6E-06 45.3 5.5 34 44-77 22-55 (284)
23 COG1039 RnhC Ribonuclease HIII 93.5 0.22 4.8E-06 43.8 6.3 40 47-86 28-67 (297)
24 PRK00996 ribonuclease HIII; Pr 93.1 0.18 4E-06 44.5 5.3 33 45-77 26-58 (304)
25 COG4871 Uncharacterized protei 91.8 1.4 2.9E-05 36.1 8.2 73 109-185 36-108 (193)
26 PRK00996 ribonuclease HIII; Pr 91.6 0.41 8.9E-06 42.3 5.6 37 136-172 26-62 (304)
27 COG1039 RnhC Ribonuclease HIII 91.4 0.54 1.2E-05 41.4 6.0 41 138-178 28-68 (297)
28 TIGR00716 rnhC ribonuclease HI 89.6 0.91 2E-05 39.8 5.9 35 135-169 22-56 (284)
29 PRK12475 thiamine/molybdopteri 86.3 3.2 7E-05 37.1 7.5 59 27-88 277-336 (338)
30 TIGR02187 GlrX_arch Glutaredox 86.0 5.7 0.00012 32.7 8.3 115 60-177 79-213 (215)
31 PRK12475 thiamine/molybdopteri 84.9 3.1 6.7E-05 37.2 6.7 34 144-179 303-336 (338)
32 PRK07688 thiamine/molybdopteri 82.8 3.7 8E-05 36.7 6.2 59 27-88 277-337 (339)
33 PRK11509 hydrogenase-1 operon 75.4 4.2 9E-05 31.8 3.7 29 152-180 94-124 (132)
34 PRK15468 carboxysome structura 74.0 6.3 0.00014 30.0 4.2 32 66-99 73-105 (111)
35 cd03065 PDI_b_Calsequestrin_N 67.9 11 0.00023 28.8 4.5 29 152-180 90-119 (120)
36 PRK07688 thiamine/molybdopteri 60.2 30 0.00065 30.9 6.5 35 145-179 303-337 (339)
37 cd02965 HyaE HyaE family; HyaE 57.8 9.6 0.00021 28.9 2.5 52 121-173 51-109 (111)
38 PLN00410 U5 snRNP protein, DIM 53.8 23 0.00049 28.0 4.1 40 144-183 73-123 (142)
39 cd03065 PDI_b_Calsequestrin_N 52.8 23 0.00049 27.0 3.9 29 60-88 89-118 (120)
40 PHA02278 thioredoxin-like prot 51.6 23 0.00049 26.0 3.6 23 152-174 75-99 (103)
41 KOG4749 Inositol polyphosphate 51.5 4.2 9E-05 36.7 -0.4 57 128-184 172-242 (375)
42 PLN00410 U5 snRNP protein, DIM 51.5 33 0.00071 27.1 4.7 62 31-92 45-123 (142)
43 KOG0910 Thioredoxin-like prote 51.0 27 0.00058 28.0 4.1 76 103-181 62-149 (150)
44 PF06277 EutA: Ethanolamine ut 50.8 89 0.0019 29.6 8.1 85 66-167 84-171 (473)
45 PRK09381 trxA thioredoxin; Pro 50.6 24 0.00053 25.1 3.6 27 153-179 79-107 (109)
46 TIGR00090 iojap_ybeB iojap-lik 50.6 34 0.00073 25.1 4.4 34 65-99 28-61 (99)
47 PRK10996 thioredoxin 2; Provis 49.2 27 0.00058 26.7 3.8 28 152-179 109-138 (139)
48 PTZ00129 40S ribosomal protein 47.3 62 0.0014 25.9 5.7 51 48-98 37-91 (149)
49 TIGR00411 redox_disulf_1 small 44.8 19 0.00041 24.0 2.1 22 158-179 60-81 (82)
50 cd02948 TRX_NDPK TRX domain, T 44.8 34 0.00073 24.4 3.6 26 152-178 74-101 (102)
51 PRK13011 formyltetrahydrofolat 43.9 1.9E+02 0.004 25.3 8.7 93 70-176 10-110 (286)
52 PRK09381 trxA thioredoxin; Pro 43.1 36 0.00079 24.2 3.5 28 61-88 78-107 (109)
53 cd02963 TRX_DnaJ TRX domain, D 42.6 31 0.00068 25.1 3.2 26 153-178 83-110 (111)
54 PF07338 DUF1471: Protein of u 42.5 32 0.00069 22.7 2.9 24 157-180 4-28 (56)
55 PF04628 Sedlin_N: Sedlin, N-t 40.9 1.1E+02 0.0024 23.3 6.1 50 136-185 49-104 (132)
56 PF06200 tify: tify domain; I 40.9 76 0.0017 19.3 4.1 28 58-85 4-31 (36)
57 PF00085 Thioredoxin: Thioredo 38.4 75 0.0016 21.6 4.5 26 153-178 75-102 (103)
58 PF02410 Oligomerisation: Olig 37.7 64 0.0014 23.5 4.2 30 67-97 30-60 (100)
59 PRK06027 purU formyltetrahydro 37.2 2.8E+02 0.006 24.1 8.7 94 70-177 9-111 (286)
60 cd07047 BMC_PduB_repeat1 1,2-p 37.2 59 0.0013 25.5 4.1 29 158-186 78-106 (134)
61 KOG0910 Thioredoxin-like prote 36.9 57 0.0012 26.1 4.0 30 60-89 117-148 (150)
62 PF13192 Thioredoxin_3: Thiore 36.8 43 0.00094 22.7 3.0 22 156-177 54-76 (76)
63 PHA02278 thioredoxin-like prot 36.0 52 0.0011 24.1 3.4 24 60-83 74-99 (103)
64 PRK11509 hydrogenase-1 operon 35.5 74 0.0016 24.8 4.4 30 60-89 93-124 (132)
65 cd02950 TxlA TRX-like protein 34.9 74 0.0016 24.4 4.3 28 153-180 80-110 (142)
66 PRK11538 ribosome-associated p 34.3 85 0.0018 23.4 4.4 33 65-98 33-65 (105)
67 cd01644 RT_pepA17 RT_pepA17: R 33.7 55 0.0012 27.2 3.6 28 72-99 145-172 (213)
68 cd02956 ybbN ybbN protein fami 33.5 56 0.0012 22.5 3.2 25 152-176 69-95 (96)
69 PRK15468 carboxysome structura 33.4 50 0.0011 25.1 3.0 31 153-185 69-99 (111)
70 PF03135 CagE_TrbE_VirB: CagE, 33.3 60 0.0013 26.3 3.7 38 61-99 144-181 (205)
71 cd02963 TRX_DnaJ TRX domain, D 32.9 53 0.0011 23.8 3.1 27 61-87 82-110 (111)
72 PRK10996 thioredoxin 2; Provis 32.9 78 0.0017 24.1 4.1 28 61-88 109-138 (139)
73 PF11869 DUF3389: Protein of u 31.9 24 0.00053 25.0 1.0 11 154-164 3-13 (75)
74 COG0533 QRI7 Metal-dependent p 31.7 1.1E+02 0.0023 27.9 5.2 46 47-92 125-171 (342)
75 cd02949 TRX_NTR TRX domain, no 31.6 68 0.0015 22.4 3.4 25 152-176 70-96 (97)
76 PRK10259 hypothetical protein; 30.7 60 0.0013 23.5 2.9 24 157-180 36-59 (86)
77 PTZ00397 macrophage migration 30.4 1.6E+02 0.0034 21.7 5.3 32 70-101 63-95 (116)
78 PF06526 DUF1107: Protein of u 29.8 86 0.0019 21.6 3.4 32 63-95 32-63 (64)
79 TIGR01068 thioredoxin thioredo 29.1 1E+02 0.0022 20.8 3.8 26 153-178 72-99 (101)
80 TIGR00385 dsbE periplasmic pro 28.7 88 0.0019 24.5 3.9 48 133-180 122-171 (173)
81 COG3445 Acid-induced glycyl ra 28.4 24 0.00052 26.6 0.5 51 116-177 70-120 (127)
82 PF10686 DUF2493: Protein of u 28.3 79 0.0017 21.8 3.1 20 160-179 5-24 (71)
83 cd02393 PNPase_KH Polynucleoti 27.6 1.4E+02 0.003 19.6 4.1 28 59-87 32-59 (61)
84 KOG3946 Glutaminyl cyclase [Po 27.6 92 0.002 27.9 4.1 58 82-146 72-138 (338)
85 cd07049 BMC_EutL_repeat1 ethan 27.4 1E+02 0.0022 23.2 3.7 28 67-95 71-100 (103)
86 KOG2360 Proliferation-associat 27.2 67 0.0015 29.8 3.3 81 43-126 277-358 (413)
87 COG4274 Uncharacterized conser 27.0 76 0.0016 23.9 3.0 60 70-129 17-78 (104)
88 PF11399 DUF3192: Protein of u 27.0 1.1E+02 0.0025 22.9 3.9 21 149-169 79-99 (102)
89 COG2221 DsrA Dissimilatory sul 26.5 43 0.00093 30.0 1.8 63 61-128 61-127 (317)
90 PF13575 DUF4135: Domain of un 26.0 59 0.0013 29.1 2.7 54 70-127 122-178 (370)
91 PF13356 DUF4102: Domain of un 25.5 2.4E+02 0.0052 19.7 5.5 52 47-99 21-80 (89)
92 cd03005 PDI_a_ERp46 PDIa famil 25.5 81 0.0018 21.6 2.9 22 153-174 77-100 (102)
93 PRK10719 eutA reactivating fac 25.3 2.7E+02 0.0058 26.5 6.9 30 137-166 143-173 (475)
94 COG2761 FrnE Predicted dithiol 25.2 1E+02 0.0022 26.4 3.8 32 149-181 183-214 (225)
95 COG0678 AHP1 Peroxiredoxin [Po 24.5 41 0.00089 27.3 1.2 32 135-166 5-45 (165)
96 PF05164 ZapA: Cell division p 24.3 1.8E+02 0.0038 20.0 4.4 39 151-189 2-40 (89)
97 PF11775 CobT_C: Cobalamin bio 24.2 1.3E+02 0.0028 25.6 4.2 49 56-107 11-59 (219)
98 cd07996 WGR_MMR_like WGR domai 24.0 1.9E+02 0.0041 19.4 4.4 33 66-98 40-72 (74)
99 COG4810 EutS Ethanolamine util 23.9 1.3E+02 0.0029 22.7 3.8 28 66-95 83-110 (121)
100 PF14657 Integrase_AP2: AP2-li 23.8 1.3E+02 0.0029 18.5 3.3 25 70-94 19-43 (46)
101 cd02988 Phd_like_VIAF Phosduci 23.7 54 0.0012 26.8 1.9 35 60-94 154-190 (192)
102 TIGR01651 CobT cobaltochelatas 23.6 1.2E+02 0.0026 29.6 4.4 46 59-107 394-439 (600)
103 CHL00041 rps11 ribosomal prote 23.3 3.1E+02 0.0067 20.7 5.8 51 48-98 22-75 (116)
104 PRK09929 hypothetical protein; 23.3 91 0.002 22.9 2.8 23 158-180 40-62 (91)
105 COG4978 Transcriptional regula 22.8 1.6E+02 0.0035 23.4 4.4 43 57-99 79-122 (153)
106 TIGR03632 bact_S11 30S ribosom 22.5 3.3E+02 0.0071 20.2 5.8 51 48-98 9-62 (108)
107 PF13098 Thioredoxin_2: Thiore 22.1 1.2E+02 0.0026 21.3 3.3 23 154-176 87-112 (112)
108 cd02394 vigilin_like_KH K homo 21.9 98 0.0021 19.9 2.5 20 158-179 42-61 (62)
109 cd07047 BMC_PduB_repeat1 1,2-p 21.7 1.5E+02 0.0033 23.3 3.9 28 67-94 78-105 (134)
110 PF00403 HMA: Heavy-metal-asso 21.4 86 0.0019 20.0 2.2 25 154-178 31-58 (62)
111 PF13382 Adenine_deam_C: Adeni 21.0 99 0.0022 25.1 2.9 57 61-126 59-122 (171)
112 KOG3384 Selenoprotein [General 20.9 64 0.0014 25.7 1.7 26 135-161 101-129 (154)
113 COG0100 RpsK Ribosomal protein 20.9 2.4E+02 0.0051 22.1 4.8 52 47-98 26-80 (129)
114 PRK05309 30S ribosomal protein 20.7 3.5E+02 0.0076 20.8 5.8 51 48-98 26-79 (128)
115 cd01554 EPT-like Enol pyruvate 20.7 37 0.00081 30.2 0.4 32 66-101 239-270 (408)
116 cd02975 PfPDO_like_N Pyrococcu 20.7 2.1E+02 0.0045 20.8 4.4 30 152-181 78-111 (113)
117 cd02950 TxlA TRX-like protein 20.3 1.9E+02 0.0042 22.1 4.3 28 61-88 79-109 (142)
118 COG2403 Predicted GTPase [Gene 20.2 5.3E+02 0.012 24.2 7.6 101 19-135 9-113 (449)
119 PF03332 PMM: Eukaryotic phosp 20.2 1.5E+02 0.0032 25.3 3.8 91 63-159 48-160 (220)
120 PF05906 DUF865: Herpesvirus-7 20.1 1.2E+02 0.0025 17.9 2.2 25 135-159 10-34 (35)
121 PF08622 Svf1: Svf1-like; Int 20.1 2.2E+02 0.0048 25.7 5.1 47 31-77 168-221 (325)
No 1
>PLN00062 TATA-box-binding protein; Provisional
Probab=100.00 E-value=2.3e-68 Score=434.84 Aligned_cols=179 Identities=94% Similarity=1.387 Sum_probs=175.2
Q ss_pred eeEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHHH
Q 029591 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYARII 92 (191)
Q Consensus 13 ~~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l 92 (191)
+|+|+|||||++++++|||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus 1 ~~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 1 VPTLQNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARII 80 (179)
T ss_pred CcEEEEEEEEEEcCCcccHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCcccceeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHHH
Q 029591 93 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 172 (191)
Q Consensus 93 ~~~g~~~~~~~~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~ 172 (191)
+++|+++++.+|+|+|||||+|++|+|||+.||..+.++++||||+||||+||+.+|+++++||+||||+|||||+++|+
T Consensus 81 ~~lg~~~~~~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~ 160 (179)
T PLN00062 81 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEI 160 (179)
T ss_pred HHcCCCcCCCccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 99999999999999999999999999999999988878999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhcccC
Q 029591 173 YTAFENIYPVLTEFRKVQQ 191 (191)
Q Consensus 173 ~~a~~~i~~~L~~~r~~~~ 191 (191)
++|++.|+|+|.+||+..|
T Consensus 161 ~~ai~~i~p~L~~~~~~~~ 179 (179)
T PLN00062 161 YTAFENIYPVLTEFRKRQQ 179 (179)
T ss_pred HHHHHHHHHHHHHhccCCC
Confidence 9999999999999998754
No 2
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=100.00 E-value=1.5e-67 Score=428.49 Aligned_cols=174 Identities=86% Similarity=1.305 Sum_probs=170.9
Q ss_pred eeEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHHH
Q 029591 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYARII 92 (191)
Q Consensus 13 ~~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l 92 (191)
+|+|+|||||++++++|||++||..++|++||||+|||+++|+++|+++++||+||||+||||+|+|+++.|+++++++|
T Consensus 1 ~~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L 80 (174)
T cd04516 1 VPKIQNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII 80 (174)
T ss_pred CCEEEEEEEEEEcCCeecHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCcccceeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHHH
Q 029591 93 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 172 (191)
Q Consensus 93 ~~~g~~~~~~~~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~ 172 (191)
+++|+++++.+|+|+|||||+|++|+|||++||..+.++++||||+||||+||+.+|+++++||+||||+|||+|+++|+
T Consensus 81 ~~~g~~~~~~~~~v~Nivat~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~ 160 (174)
T cd04516 81 QKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEI 160 (174)
T ss_pred HHcCCCCCCCceEEEEEEEEEECCCcccHHHHHHhChhccEeCCccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 99999999999999999999999999999999998878999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhh
Q 029591 173 YTAFENIYPVLTEF 186 (191)
Q Consensus 173 ~~a~~~i~~~L~~~ 186 (191)
++|++.|+|+|.+|
T Consensus 161 ~~a~~~i~p~L~~~ 174 (174)
T cd04516 161 YQAFENIYPILLQF 174 (174)
T ss_pred HHHHHHHHHHHhhC
Confidence 99999999999986
No 3
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=100.00 E-value=3.9e-66 Score=414.50 Aligned_cols=179 Identities=44% Similarity=0.738 Sum_probs=172.4
Q ss_pred cCCeeEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHH
Q 029591 10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYA 89 (191)
Q Consensus 10 ~~~~~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~ 89 (191)
.+.+++|+|||||.+|+++|||++++..++|+||||++||||+||+++|+++++||+|||++||||||.+|++.|+++++
T Consensus 4 ~~~~i~IeNIVAS~~L~~elDL~~~~~~l~~aeYnP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGaKs~ed~~~av~~~~ 83 (185)
T COG2101 4 SEPTITIENIVASVDLGQELDLEEVALDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGAKSVEDVHRAVKKLA 83 (185)
T ss_pred CCCccEEEEEEEEechhhhccHHHHHhhCCCCccCHhHCCeeEEEecCCcceEEEEecCcEEEeccCcHHHHHHHHHHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCCccc-ceeEEeEEEEEEcCCccChhHHHHhcCC-ccccccCCCceeEEEecCCeEEEEEeecceEEEeccC
Q 029591 90 RIIQKLGFPAKFK-DFKIQNIVGSCDVKFPIRLEGLAYSHGA-FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAK 167 (191)
Q Consensus 90 ~~l~~~g~~~~~~-~~~i~Nivat~~l~~~i~L~~la~~~~~-~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGak 167 (191)
++|++.|+++.+. +++|||||||+|+++++||+.+|..++- +++|||||||||+||+.+|++++|||+|||+||||||
T Consensus 84 ~~L~~~g~~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK 163 (185)
T COG2101 84 KKLKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAK 163 (185)
T ss_pred HHHHhcCcCcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCC
Confidence 9999999998765 8999999999999999999999998873 5999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHhhhc
Q 029591 168 VRDETYTAFENIYPVLTEFRK 188 (191)
Q Consensus 168 s~~~~~~a~~~i~~~L~~~r~ 188 (191)
+++|+++|+++|++.|.++..
T Consensus 164 ~~ed~~~Av~~i~~~L~elgl 184 (185)
T COG2101 164 SEEDAEQAVEKIQSRLEELGL 184 (185)
T ss_pred CHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999998753
No 4
>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=100.00 E-value=5.8e-66 Score=419.44 Aligned_cols=182 Identities=76% Similarity=1.210 Sum_probs=179.2
Q ss_pred cCCeeEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHH
Q 029591 10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYA 89 (191)
Q Consensus 10 ~~~~~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~ 89 (191)
++++|.++||||+++++|+|||.+||+..+|+||||++|+++++|+++|+++++||+||||+||||+|+++|+.|+++++
T Consensus 19 ~~i~~~l~nivc~~~~~c~ldLk~ial~~~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~a 98 (200)
T KOG3302|consen 19 SGLDPTLQNIVCTVNLNCKLDLKEIALHARNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKYA 98 (200)
T ss_pred cccceEEEeEEEEEeccceecHHHHhhhccccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCCcccceeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCH
Q 029591 90 RIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR 169 (191)
Q Consensus 90 ~~l~~~g~~~~~~~~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~ 169 (191)
|+||++|++++|.||++|||+||||++|+|+||+++..|+.+++||||+||||+|||.+|+++++||+||||++|||++.
T Consensus 99 RilqkLgf~~~f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~ 178 (200)
T KOG3302|consen 99 RILQKLGFPVKFRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVR 178 (200)
T ss_pred HHHHHcCCCceehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcccC
Q 029591 170 DETYTAFENIYPVLTEFRKVQQ 191 (191)
Q Consensus 170 ~~~~~a~~~i~~~L~~~r~~~~ 191 (191)
+|+.+|+++|+|+|.+|||..+
T Consensus 179 ~~i~~Ai~~IyPil~~frk~~~ 200 (200)
T KOG3302|consen 179 EETYEAIENIYPILLEFRKKLL 200 (200)
T ss_pred HHHHHHHHHHhHHHHHhhhccC
Confidence 9999999999999999998764
No 5
>PRK00394 transcription factor; Reviewed
Probab=100.00 E-value=1.8e-64 Score=412.23 Aligned_cols=175 Identities=43% Similarity=0.709 Sum_probs=169.3
Q ss_pred eEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHHHH
Q 029591 14 SSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYARIIQ 93 (191)
Q Consensus 14 ~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l~ 93 (191)
++|+|||||++++++|||++||..++|++|||++|||+++|+++|+++++||+||||+||||+|+++++.|+++++++|+
T Consensus 1 i~i~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~S~~~a~~a~~~~~~~l~ 80 (179)
T PRK00394 1 IKIENIVASTDLGQELDLEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAKSVEDLHEAVKIIIKKLK 80 (179)
T ss_pred CEEEEEEEEEEcCCCcCHHHHHhhCCCceeCcccCceEEEEecCCceEEEEEcCCcEEEEccCCHHHHHHHHHHHHHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCCc-ccceeEEeEEEEEEcCCccChhHHHHhcC-CccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHH
Q 029591 94 KLGFPAK-FKDFKIQNIVGSCDVKFPIRLEGLAYSHG-AFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDE 171 (191)
Q Consensus 94 ~~g~~~~-~~~~~i~Nivat~~l~~~i~L~~la~~~~-~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~ 171 (191)
++|+++. ..+|+|+|||||++++++|||+.+|..++ ++++||||+||||+||+.+|+++++||+||||+||||||++|
T Consensus 81 ~~g~~~~~~~~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~ 160 (179)
T PRK00394 81 ELGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEED 160 (179)
T ss_pred HcCCCccCCCceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHH
Confidence 9999885 67999999999999999999999998863 589999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhc
Q 029591 172 TYTAFENIYPVLTEFRK 188 (191)
Q Consensus 172 ~~~a~~~i~~~L~~~r~ 188 (191)
+++|+++|+|.|.++..
T Consensus 161 ~~~a~~~i~~~l~~~g~ 177 (179)
T PRK00394 161 AEKAVEKILEKLEELGL 177 (179)
T ss_pred HHHHHHHHHHHHHHcCC
Confidence 99999999999998864
No 6
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=100.00 E-value=1.6e-64 Score=410.86 Aligned_cols=173 Identities=74% Similarity=1.168 Sum_probs=169.0
Q ss_pred eeEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHHH
Q 029591 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYARII 92 (191)
Q Consensus 13 ~~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l 92 (191)
.++|+||||++++++++||++||..++|++||||+|||+++|+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus 1 ~~~i~NvVas~~l~~~idL~~la~~~~n~~YePe~fpgli~R~~~P~~t~lIf~sGKivitGaks~~~~~~a~~~~~~~L 80 (174)
T cd00652 1 SPKIQNIVATVNLGCELDLRKIALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGAKSEEDAKLAARKYARIL 80 (174)
T ss_pred CcEEEEEEEEEEcCCccCHHHHHhhCCCcEECCCccceEEEEcCCCcEEEEEECCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCC-cccceeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHH
Q 029591 93 QKLGFPA-KFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDE 171 (191)
Q Consensus 93 ~~~g~~~-~~~~~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~ 171 (191)
+++|+++ ++.+|+|+|||||++++++|||++||..++++++||||+||||+||+.+|++|++||+||||+||||||++|
T Consensus 81 ~~~g~~~~~~~~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~ 160 (174)
T cd00652 81 QKLGFPVEKFPEFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSRED 160 (174)
T ss_pred HHcCCCccccCceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHH
Confidence 9999987 888999999999999999999999999987799999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHh
Q 029591 172 TYTAFENIYPVLTE 185 (191)
Q Consensus 172 ~~~a~~~i~~~L~~ 185 (191)
+++|++.|+|+|.+
T Consensus 161 ~~~a~~~i~~~L~~ 174 (174)
T cd00652 161 IYEAVEKIYPILKE 174 (174)
T ss_pred HHHHHHHHHHHHhC
Confidence 99999999999974
No 7
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=100.00 E-value=2.6e-64 Score=409.50 Aligned_cols=173 Identities=43% Similarity=0.733 Sum_probs=167.6
Q ss_pred eeEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHHH
Q 029591 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYARII 92 (191)
Q Consensus 13 ~~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l 92 (191)
.++|+|||||++++++|||++||..++|+||||++|||+++|+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus 1 ~~~I~NvVas~~l~~~ldL~~la~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGaks~~~a~~a~~~~~~~L 80 (174)
T cd04518 1 SLKIENIVASVDLGQELDLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGAKSVEDLHRAVKEIIKKL 80 (174)
T ss_pred CcEEEEEEEEEEcCCeecHHHHHhhCCCcEECCCcCcEEEEEccCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHH
Confidence 37999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCc-ccceeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHH
Q 029591 93 QKLGFPAK-FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDE 171 (191)
Q Consensus 93 ~~~g~~~~-~~~~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~ 171 (191)
+++|+++. ..+|+|+|||||++++++|||+.++..++ +++||||+||||+||+.+|+++++||+||||+||||||++|
T Consensus 81 ~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~la~~~~-~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~ 159 (174)
T cd04518 81 KDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIGLP-NAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEED 159 (174)
T ss_pred HhcCCCccCCCceEEEEEEEEEEcCCccCHHHHHhhCC-CCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHH
Confidence 99999874 46899999999999999999999999886 99999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhh
Q 029591 172 TYTAFENIYPVLTEF 186 (191)
Q Consensus 172 ~~~a~~~i~~~L~~~ 186 (191)
+++|++.|+|.|.++
T Consensus 160 ~~~a~~~i~~~l~~~ 174 (174)
T cd04518 160 AKRAVEKLLSRLKEL 174 (174)
T ss_pred HHHHHHHHHHHHhhC
Confidence 999999999999874
No 8
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=100.00 E-value=9.1e-64 Score=406.43 Aligned_cols=173 Identities=45% Similarity=0.849 Sum_probs=168.6
Q ss_pred CeeEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHH
Q 029591 12 AVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYARI 91 (191)
Q Consensus 12 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~ 91 (191)
++++|+||||+++++++|||+++|..++|++||| +|||+++|+++|+++++||+|||++|||++|+++++.|+++++++
T Consensus 1 ~~~~i~Nvvas~~l~~~idL~~la~~l~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~ 79 (174)
T cd04517 1 LDILIVNVVCQFSLRCHIDLRKLALAGRNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARL 79 (174)
T ss_pred CccEEEEEEEEEEcCCcccHHHHHhhCCCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHH
Confidence 4689999999999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCC-cccceeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHH
Q 029591 92 IQKLGFPA-KFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRD 170 (191)
Q Consensus 92 l~~~g~~~-~~~~~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~ 170 (191)
|+++|++. ++.+|+|+|||||+++||+|||++|+..+.++++||||+||||+||+.+|++|++||+||||+|||+|+++
T Consensus 80 l~~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~ 159 (174)
T cd04517 80 LQKLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSME 159 (174)
T ss_pred HHHcCCCcccCCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHH
Confidence 99999986 88999999999999999999999999988789999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHh
Q 029591 171 ETYTAFENIYPVLTE 185 (191)
Q Consensus 171 ~~~~a~~~i~~~L~~ 185 (191)
|+++|++.|+|+|.+
T Consensus 160 ~~~~a~~~i~pil~~ 174 (174)
T cd04517 160 DVREAVEKIYPIVFE 174 (174)
T ss_pred HHHHHHHHHHHHHhC
Confidence 999999999999974
No 9
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=99.97 E-value=2.5e-31 Score=193.05 Aligned_cols=86 Identities=56% Similarity=0.864 Sum_probs=80.9
Q ss_pred ccceeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHHHHHHHHHHH
Q 029591 101 FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIY 180 (191)
Q Consensus 101 ~~~~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~~i~ 180 (191)
|.+++|+||||+++++++|||++||..+ ++++||||+|||++||+.+|+++++||+||||+||||+|++++++|+++++
T Consensus 1 ~~~~~i~NIva~~~l~~~idL~~la~~~-~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~ 79 (86)
T PF00352_consen 1 FPDFKIVNIVASFDLPFEIDLEELAEEL-ENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKIL 79 (86)
T ss_dssp -EEEEEEEEEEEEE-SSEB-HHHHHHHS-TTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHH
T ss_pred CCccEEEEEEEEEECCCccCHHHHHhhc-cCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHH
Confidence 5689999999999999999999999998 699999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhh
Q 029591 181 PVLTEFR 187 (191)
Q Consensus 181 ~~L~~~r 187 (191)
|+|.+++
T Consensus 80 ~~L~~~~ 86 (86)
T PF00352_consen 80 PILQKLG 86 (86)
T ss_dssp HHHHHTT
T ss_pred HHHHHcC
Confidence 9999985
No 10
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=99.97 E-value=5.8e-31 Score=191.11 Aligned_cols=84 Identities=48% Similarity=0.745 Sum_probs=80.6
Q ss_pred eeEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHHH
Q 029591 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYARII 92 (191)
Q Consensus 13 ~~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l 92 (191)
+++|+||||+++++++|||++||..++|++||||+|||+++|+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus 3 ~~~i~NIva~~~l~~~idL~~la~~~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 3 DFKIVNIVASFDLPFEIDLEELAEELENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKILPIL 82 (86)
T ss_dssp EEEEEEEEEEEE-SSEB-HHHHHHHSTTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred ccEEEEEEEEEECCCccCHHHHHhhccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcC
Q 029591 93 QKLG 96 (191)
Q Consensus 93 ~~~g 96 (191)
+++|
T Consensus 83 ~~~~ 86 (86)
T PF00352_consen 83 QKLG 86 (86)
T ss_dssp HHTT
T ss_pred HHcC
Confidence 9986
No 11
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=99.96 E-value=4.2e-29 Score=200.83 Aligned_cols=87 Identities=37% Similarity=0.637 Sum_probs=83.2
Q ss_pred CCeeEEEEEEEEEEcCCccCHHHHHhhCCC--ceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHH
Q 029591 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARN--AEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKY 88 (191)
Q Consensus 11 ~~~~~I~NvVas~~l~~~ldL~~la~~~~n--~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i 88 (191)
...++|||||||+||+..+||+.+|..+++ +||||||||||+||+.+|++.++||+|||++|||||+++|++.|++++
T Consensus 96 ~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~ed~~~Av~~i 175 (185)
T COG2101 96 EPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKI 175 (185)
T ss_pred CCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCHHHHHHHHHHH
Confidence 357899999999999999999999998865 999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCC
Q 029591 89 ARIIQKLGF 97 (191)
Q Consensus 89 ~~~l~~~g~ 97 (191)
.+.|+++|.
T Consensus 176 ~~~L~elgl 184 (185)
T COG2101 176 QSRLEELGL 184 (185)
T ss_pred HHHHHHhcc
Confidence 999999874
No 12
>PRK00394 transcription factor; Reviewed
Probab=99.96 E-value=2.4e-28 Score=199.57 Aligned_cols=87 Identities=38% Similarity=0.669 Sum_probs=84.4
Q ss_pred CCeeEEEEEEEEEEcCCccCHHHHHhhC--CCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHH
Q 029591 11 GAVSSVKNIVSTVNLDCKLDLKKIALQA--RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKY 88 (191)
Q Consensus 11 ~~~~~I~NvVas~~l~~~ldL~~la~~~--~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i 88 (191)
..+++|+|||||++++++|||+.+|..+ +|++||||+||||+||+.+|+++++||+||||+||||+|++|++.|++++
T Consensus 89 ~~~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i 168 (179)
T PRK00394 89 EPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDAEKAVEKI 168 (179)
T ss_pred CCceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHH
Confidence 4689999999999999999999999987 89999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCC
Q 029591 89 ARIIQKLGF 97 (191)
Q Consensus 89 ~~~l~~~g~ 97 (191)
.++|+++|.
T Consensus 169 ~~~l~~~g~ 177 (179)
T PRK00394 169 LEKLEELGL 177 (179)
T ss_pred HHHHHHcCC
Confidence 999999986
No 13
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=99.95 E-value=5.1e-28 Score=196.81 Aligned_cols=85 Identities=41% Similarity=0.652 Sum_probs=82.2
Q ss_pred CCeeEEEEEEEEEEcCCccCHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHH
Q 029591 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYAR 90 (191)
Q Consensus 11 ~~~~~I~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~ 90 (191)
..+++|+|||||++++++|||+.+|..++|++||||+||||+||+.+|+++++||+||||+||||+|++|++.|++++.+
T Consensus 90 ~~~~~i~NIVas~~l~~~i~L~~la~~~~~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~~ 169 (174)
T cd04518 90 KPEIKVQNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDAKRAVEKLLS 169 (174)
T ss_pred CCceEEEEEEEEEEcCCccCHHHHHhhCCCCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHc
Q 029591 91 IIQKL 95 (191)
Q Consensus 91 ~l~~~ 95 (191)
+|+++
T Consensus 170 ~l~~~ 174 (174)
T cd04518 170 RLKEL 174 (174)
T ss_pred HHhhC
Confidence 99864
No 14
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=99.94 E-value=1.4e-26 Score=188.37 Aligned_cols=83 Identities=34% Similarity=0.541 Sum_probs=79.5
Q ss_pred eeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHHHHHHHHHHHHHH
Q 029591 104 FKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL 183 (191)
Q Consensus 104 ~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L 183 (191)
++|+|||||++++++|||++||..+ ++++||||+|||++||+.+|+++++||+||||+||||+|+++++.|++++.++|
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L 80 (174)
T cd04516 2 PKIQNIVATVNLGCKLDLKKIALRA-RNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII 80 (174)
T ss_pred CEEEEEEEEEEcCCeecHHHHHhhC-CCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 6899999999999999999999876 589999999999999999999999999999999999999999999999999999
Q ss_pred Hhhh
Q 029591 184 TEFR 187 (191)
Q Consensus 184 ~~~r 187 (191)
+++-
T Consensus 81 ~~~g 84 (174)
T cd04516 81 QKLG 84 (174)
T ss_pred HHcC
Confidence 8764
No 15
>PLN00062 TATA-box-binding protein; Provisional
Probab=99.94 E-value=2.3e-26 Score=187.85 Aligned_cols=83 Identities=30% Similarity=0.518 Sum_probs=79.3
Q ss_pred eeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHHHHHHHHHHHHHH
Q 029591 104 FKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL 183 (191)
Q Consensus 104 ~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L 183 (191)
++|+|||||++++++|||++|+..+ ++++||||+|||++||+.+|+++++||+||||+||||+|+++++.|++++.++|
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 2 PTLQNIVSTVNLDCKLDLKKIALQA-RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARII 80 (179)
T ss_pred cEEEEEEEEEEcCCcccHHHHHhhC-CCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 6899999999999999999999876 589999999999999999999999999999999999999999999999999999
Q ss_pred Hhhh
Q 029591 184 TEFR 187 (191)
Q Consensus 184 ~~~r 187 (191)
.++-
T Consensus 81 ~~lg 84 (179)
T PLN00062 81 QKLG 84 (179)
T ss_pred HHcC
Confidence 8753
No 16
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=99.93 E-value=4.2e-26 Score=185.53 Aligned_cols=85 Identities=39% Similarity=0.557 Sum_probs=81.1
Q ss_pred cCCeeEEEEEEEEEEcCCccCHHHHHhhCC-CceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHH
Q 029591 10 LGAVSSVKNIVSTVNLDCKLDLKKIALQAR-NAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKY 88 (191)
Q Consensus 10 ~~~~~~I~NvVas~~l~~~ldL~~la~~~~-n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i 88 (191)
+..+++|+||||+++++++|||+.||..++ |++||||+|||++||+.+|+++++||+||||+||||+|++|++.|++++
T Consensus 89 ~~~~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i 168 (174)
T cd00652 89 KFPEFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKI 168 (174)
T ss_pred ccCceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHH
Confidence 346899999999999999999999999986 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHH
Q 029591 89 ARIIQK 94 (191)
Q Consensus 89 ~~~l~~ 94 (191)
.++|.+
T Consensus 169 ~~~L~~ 174 (174)
T cd00652 169 YPILKE 174 (174)
T ss_pred HHHHhC
Confidence 998863
No 17
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=99.92 E-value=7.3e-25 Score=178.28 Aligned_cols=83 Identities=29% Similarity=0.470 Sum_probs=79.3
Q ss_pred ceeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHHHHHHHHHHHHH
Q 029591 103 DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPV 182 (191)
Q Consensus 103 ~~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~ 182 (191)
+++|+||||+++++++|||++++..+ ++++||| +|||++||+.+|+++++||+||||+|||++|.++++.|++++.++
T Consensus 2 ~~~i~Nvvas~~l~~~idL~~la~~l-~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~ 79 (174)
T cd04517 2 DILIVNVVCQFSLRCHIDLRKLALAG-RNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARL 79 (174)
T ss_pred ccEEEEEEEEEEcCCcccHHHHHhhC-CCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHH
Confidence 58999999999999999999999877 5999999 999999999999999999999999999999999999999999999
Q ss_pred HHhhh
Q 029591 183 LTEFR 187 (191)
Q Consensus 183 L~~~r 187 (191)
|.++-
T Consensus 80 l~~~g 84 (174)
T cd04517 80 LQKLG 84 (174)
T ss_pred HHHcC
Confidence 98754
No 18
>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=99.84 E-value=1.4e-20 Score=153.77 Aligned_cols=86 Identities=28% Similarity=0.460 Sum_probs=81.8
Q ss_pred CeeEEEEEEEEEEcCCccCHHHHHhhC-CCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHH
Q 029591 12 AVSSVKNIVSTVNLDCKLDLKKIALQA-RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYAR 90 (191)
Q Consensus 12 ~~~~I~NvVas~~l~~~ldL~~la~~~-~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~ 90 (191)
++++|+|||||||+.++|+|+.++... ..+.||||.||||+||+.+|+++++||.||||++|||++.++.+.|+++|..
T Consensus 111 ~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~~~i~~Ai~~IyP 190 (200)
T KOG3302|consen 111 RDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVREETYEAIENIYP 190 (200)
T ss_pred hheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccHHHHHHHHHHHhH
Confidence 689999999999999999999999877 5799999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCC
Q 029591 91 IIQKLGF 97 (191)
Q Consensus 91 ~l~~~g~ 97 (191)
+|.++..
T Consensus 191 il~~frk 197 (200)
T KOG3302|consen 191 ILLEFRK 197 (200)
T ss_pred HHHHhhh
Confidence 9988743
No 19
>PF11858 DUF3378: Domain of unknown function (DUF3378); InterPro: IPR024568 Ribonuclease HIII 3.1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other []. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This entry represents the uncharacterised N-terminal domain of bacterial RNase HIII.; PDB: 3ASM_A 2D0C_A 2D0B_A 2D0A_A.
Probab=96.77 E-value=0.0018 Score=46.62 Aligned_cols=32 Identities=22% Similarity=0.342 Sum_probs=27.3
Q ss_pred CCceEEEEecCCceEEEEecCceEEEeccCCH
Q 029591 47 RFAAVIMRIREPKTTALIFASGKMVCTGAKSE 78 (191)
Q Consensus 47 ~fpglv~R~~~P~~t~lIf~SGKivitGaks~ 78 (191)
.=|+++++.+.+.+++++|.|||++..|...+
T Consensus 27 ~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~~Ae 58 (81)
T PF11858_consen 27 KPPYAVFQAKYNGVTITAYKSGKVVFQGKNAE 58 (81)
T ss_dssp --TTEEEEEEETTEEEEEETTSEEEEESTTHH
T ss_pred CCCCEEEEEeCCCeEEEEEeCCeEEEECCCHH
Confidence 34899999999999999999999999996443
No 20
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=96.59 E-value=0.017 Score=46.93 Aligned_cols=63 Identities=25% Similarity=0.288 Sum_probs=53.9
Q ss_pred CHHHHHhhCCCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHHHHHc
Q 029591 30 DLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYARIIQKL 95 (191)
Q Consensus 30 dL~~la~~~~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l~~~ 95 (191)
=|.-||..++++.|..++ ..++++.- ..-++||.|||+..|-.+++++|+..+..+.+++++.
T Consensus 47 ilplla~l~P~anY~~kk-~~l~~~kg--erIitiy~sGkVsm~~ikdedEAkeilgel~d~ineA 109 (193)
T COG4871 47 ILPLLAPLFPRANYSDKK-NILILQKG--ERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINEA 109 (193)
T ss_pred hHHHhHhhCCCccccccc-ceEEEeec--cEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHHH
Confidence 356678888999999886 67777754 4678899999999999999999999999999998873
No 21
>PF11858 DUF3378: Domain of unknown function (DUF3378); InterPro: IPR024568 Ribonuclease HIII 3.1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other []. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This entry represents the uncharacterised N-terminal domain of bacterial RNase HIII.; PDB: 3ASM_A 2D0C_A 2D0B_A 2D0A_A.
Probab=95.76 E-value=0.012 Score=42.39 Aligned_cols=36 Identities=22% Similarity=0.391 Sum_probs=30.4
Q ss_pred CCceeEEEecCCeEEEEEeecceEEEeccCCHHHHH
Q 029591 138 LFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETY 173 (191)
Q Consensus 138 ~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~~ 173 (191)
.=||..|+...+.+|+.++.||||++-|...+.++.
T Consensus 27 ~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~~Ae~~A~ 62 (81)
T PF11858_consen 27 KPPYAVFQAKYNGVTITAYKSGKVVFQGKNAEQEAA 62 (81)
T ss_dssp --TTEEEEEEETTEEEEEETTSEEEEESTTHHHHHH
T ss_pred CCCCEEEEEeCCCeEEEEEeCCeEEEECCCHHHHHH
Confidence 348999999999999999999999999997765543
No 22
>TIGR00716 rnhC ribonuclease HIII. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III.
Probab=93.95 E-value=0.12 Score=45.33 Aligned_cols=34 Identities=18% Similarity=0.369 Sum_probs=29.2
Q ss_pred cCCCCceEEEEecCCceEEEEecCceEEEeccCC
Q 029591 44 NPKRFAAVIMRIREPKTTALIFASGKMVCTGAKS 77 (191)
Q Consensus 44 ePe~fpglv~R~~~P~~t~lIf~SGKivitGaks 77 (191)
.+..=|+.+++.+.|.+|+.+|.|||++..|...
T Consensus 22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~a 55 (284)
T TIGR00716 22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNS 55 (284)
T ss_pred ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCH
Confidence 4445689999999999999999999999999443
No 23
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=93.48 E-value=0.22 Score=43.85 Aligned_cols=40 Identities=25% Similarity=0.322 Sum_probs=33.8
Q ss_pred CCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHH
Q 029591 47 RFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAAR 86 (191)
Q Consensus 47 ~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~ 86 (191)
..|+.+++.+.|.+++.+|.|||+++.|--.++-+..=..
T Consensus 28 ~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~ 67 (297)
T COG1039 28 NPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLN 67 (297)
T ss_pred CCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhh
Confidence 6789999999999999999999999999666655555444
No 24
>PRK00996 ribonuclease HIII; Provisional
Probab=93.10 E-value=0.18 Score=44.53 Aligned_cols=33 Identities=24% Similarity=0.435 Sum_probs=28.5
Q ss_pred CCCCceEEEEecCCceEEEEecCceEEEeccCC
Q 029591 45 PKRFAAVIMRIREPKTTALIFASGKMVCTGAKS 77 (191)
Q Consensus 45 Pe~fpglv~R~~~P~~t~lIf~SGKivitGaks 77 (191)
+..-|+.+++.+.+.+++.+|.|||++..|...
T Consensus 26 ~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~a 58 (304)
T PRK00996 26 PSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGA 58 (304)
T ss_pred cCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCH
Confidence 344578999999999999999999999999543
No 25
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=91.79 E-value=1.4 Score=36.06 Aligned_cols=73 Identities=22% Similarity=0.244 Sum_probs=57.3
Q ss_pred EEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHHHHHHHHHHHHHHHh
Q 029591 109 IVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTE 185 (191)
Q Consensus 109 ivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L~~ 185 (191)
+.+..+-+++=-|..|+..++ .+.|.-.. .-|++..-+ .-+.|+.||||.+|--++++++.+.+..+..++.+
T Consensus 36 Vi~~md~~lg~ilplla~l~P-~anY~~kk-~~l~~~kge--rIitiy~sGkVsm~~ikdedEAkeilgel~d~ine 108 (193)
T COG4871 36 VIANMDPPLGGILPLLAPLFP-RANYSDKK-NILILQKGE--RIITIYGSGKVSMTMIKDEDEAKEILGELMDIINE 108 (193)
T ss_pred EEeecCCCcchhHHHhHhhCC-Cccccccc-ceEEEeecc--EEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHH
Confidence 556666666666788888774 68998554 666666444 44679999999999999999999999999988775
No 26
>PRK00996 ribonuclease HIII; Provisional
Probab=91.56 E-value=0.41 Score=42.33 Aligned_cols=37 Identities=30% Similarity=0.611 Sum_probs=30.9
Q ss_pred cCCCceeEEEecCCeEEEEEeecceEEEeccCCHHHH
Q 029591 136 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 172 (191)
Q Consensus 136 Pe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~ 172 (191)
+..-|+..|+...+.+++.++.||||++.|...++++
T Consensus 26 ~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae~~~ 62 (304)
T PRK00996 26 PSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAEAFA 62 (304)
T ss_pred cCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHHHHH
Confidence 4456899999999999999999999999996554333
No 27
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=91.38 E-value=0.54 Score=41.43 Aligned_cols=41 Identities=24% Similarity=0.369 Sum_probs=36.2
Q ss_pred CCceeEEEecCCeEEEEEeecceEEEeccCCHHHHHHHHHH
Q 029591 138 LFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFEN 178 (191)
Q Consensus 138 ~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~~ 178 (191)
.-|+.+|....|.+|+.++.|||+++-|-..++.+.+-...
T Consensus 28 ~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~~ 68 (297)
T COG1039 28 NPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLNP 68 (297)
T ss_pred CCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhhh
Confidence 56899999999999999999999999999988777766554
No 28
>TIGR00716 rnhC ribonuclease HIII. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III.
Probab=89.55 E-value=0.91 Score=39.79 Aligned_cols=35 Identities=20% Similarity=0.439 Sum_probs=30.2
Q ss_pred ccCCCceeEEEecCCeEEEEEeecceEEEeccCCH
Q 029591 135 EPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR 169 (191)
Q Consensus 135 ePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~ 169 (191)
++..=||..|+...+.+|+.++.||||++-|...+
T Consensus 22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~ae 56 (284)
T TIGR00716 22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNSE 56 (284)
T ss_pred ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCHH
Confidence 45556899999999999999999999999995443
No 29
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=86.29 E-value=3.2 Score=37.07 Aligned_cols=59 Identities=14% Similarity=0.362 Sum_probs=42.5
Q ss_pred CccCHHHHHhhCCC-ceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHH
Q 029591 27 CKLDLKKIALQARN-AEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKY 88 (191)
Q Consensus 27 ~~ldL~~la~~~~n-~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i 88 (191)
..+|+++++..+.. ..++.-.| .+.++.. .-.+.+|+.|++++.|.+++.+|+.-.+++
T Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~~f~~gr~~~~g~~~~~~a~~~~~~~ 336 (338)
T PRK12475 277 RRLNLEEIKKRLQKIGKVDANPY-LLSFQLD--EYRFVLFTDGRAFIHGTNDIKKAKRLYARY 336 (338)
T ss_pred CccCHHHHHHHHhhcCEEEeccc-EEEEEEC--CEEEEEEcCCcEEEECCCCHHHHHHHHHHh
Confidence 57999999876632 23333222 3445544 478999999999999999999999876654
No 30
>TIGR02187 GlrX_arch Glutaredoxin-like domain protein. This family of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different.
Probab=85.97 E-value=5.7 Score=32.71 Aligned_cols=115 Identities=16% Similarity=0.132 Sum_probs=63.2
Q ss_pred eEEEEecCceEE---EeccCCHHHHHHHHHHHHHHHHHcC--CCC-------ccc-ceeEEeEEEEEEcCCcc---ChhH
Q 029591 60 TTALIFASGKMV---CTGAKSEQQSKLAARKYARIIQKLG--FPA-------KFK-DFKIQNIVGSCDVKFPI---RLEG 123 (191)
Q Consensus 60 ~t~lIf~SGKiv---itGaks~e~a~~a~~~i~~~l~~~g--~~~-------~~~-~~~i~Nivat~~l~~~i---~L~~ 123 (191)
-|+.+|.+|+.+ ..|..+.++...-++.+... ..-+ ++. ... ...|.-..++.+-+++. -++.
T Consensus 79 Pt~~~f~~g~~~~~~~~G~~~~~~l~~~i~~~~~~-~~~~~~L~~~~~~~l~~~~~pv~I~~F~a~~C~~C~~~~~~l~~ 157 (215)
T TIGR02187 79 PTTIILEEGKDGGIRYTGIPAGYEFAALIEDIVRV-SQGEPGLSEKTVELLQSLDEPVRIEVFVTPTCPYCPYAVLMAHK 157 (215)
T ss_pred CEEEEEeCCeeeEEEEeecCCHHHHHHHHHHHHHh-cCCCCCCCHHHHHHHHhcCCCcEEEEEECCCCCCcHHHHHHHHH
Confidence 388999999885 46988887776655555322 1111 111 011 22333233444433431 2344
Q ss_pred HHHhcCC--ccccccCCCceeE--EEecCCeEEEEEeecceEEEeccCCHHHHHHHHH
Q 029591 124 LAYSHGA--FSSYEPELFPGLI--YRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFE 177 (191)
Q Consensus 124 la~~~~~--~~~YePe~fpgli--~r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~ 177 (191)
++.+.+. ...+|++.+|.+. |++.. --|+++|..|+. +.|..+.+++.+.+.
T Consensus 158 l~~~~~~i~~~~vD~~~~~~~~~~~~V~~-vPtl~i~~~~~~-~~G~~~~~~l~~~l~ 213 (215)
T TIGR02187 158 FALANDKILGEMIEANENPDLAEKYGVMS-VPKIVINKGVEE-FVGAYPEEQFLEYIL 213 (215)
T ss_pred HHHhcCceEEEEEeCCCCHHHHHHhCCcc-CCEEEEecCCEE-EECCCCHHHHHHHHH
Confidence 4433321 2346677777654 33321 125677888875 899999988877765
No 31
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=84.92 E-value=3.1 Score=37.16 Aligned_cols=34 Identities=12% Similarity=0.408 Sum_probs=28.3
Q ss_pred EEecCCeEEEEEeecceEEEeccCCHHHHHHHHHHH
Q 029591 144 YRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENI 179 (191)
Q Consensus 144 ~r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~~i 179 (191)
++..+ -.+.+|++|+++|-|.+++.+++.-++++
T Consensus 303 ~~~~~--~~~~~f~~gr~~~~g~~~~~~a~~~~~~~ 336 (338)
T PRK12475 303 FQLDE--YRFVLFTDGRAFIHGTNDIKKAKRLYARY 336 (338)
T ss_pred EEECC--EEEEEEcCCcEEEECCCCHHHHHHHHHHh
Confidence 55544 56789999999999999999998877754
No 32
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=82.75 E-value=3.7 Score=36.70 Aligned_cols=59 Identities=19% Similarity=0.373 Sum_probs=43.9
Q ss_pred CccCHHHHHhhCCCc--eecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHH
Q 029591 27 CKLDLKKIALQARNA--EYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKY 88 (191)
Q Consensus 27 ~~ldL~~la~~~~n~--eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i 88 (191)
..+++++++..+... ++.. +.+.++++.+.-.+..|++|++++.|++++.+|+.-..++
T Consensus 277 ~~i~~~~~~~~l~~~~~~~~~---~~~ll~vr~~~~~~~~~~~gr~~i~g~~~~~~a~~~~~~~ 337 (339)
T PRK07688 277 EEYDLEELAELLRDRGLDVNV---NPYLLSFSLEEKRLVLFKDGRVLVHGTKDISEAKTIYHRY 337 (339)
T ss_pred CccCHHHHHHHHHhcccccCC---CcEEEEEecCCeEEEEEcCCCEEEECCCCHHHHHHHHHHh
Confidence 457788887766332 3333 3456677777799999999999999999999998866654
No 33
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=75.39 E-value=4.2 Score=31.84 Aligned_cols=29 Identities=17% Similarity=0.335 Sum_probs=24.1
Q ss_pred EEEEeecceEE--EeccCCHHHHHHHHHHHH
Q 029591 152 VLLIFVSGKIV--ITGAKVRDETYTAFENIY 180 (191)
Q Consensus 152 t~lIF~sGkiv--itGaks~~~~~~a~~~i~ 180 (191)
|+++|.+|+.+ +.|..+.+++.+-++.++
T Consensus 94 TLl~FkdGk~v~~i~G~~~k~~l~~~I~~~L 124 (132)
T PRK11509 94 ATLVFTGGNYRGVLNGIHPWAELINLMRGLV 124 (132)
T ss_pred EEEEEECCEEEEEEeCcCCHHHHHHHHHHHh
Confidence 78999999996 789999988887777554
No 34
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=73.98 E-value=6.3 Score=29.97 Aligned_cols=32 Identities=22% Similarity=0.224 Sum_probs=28.3
Q ss_pred cCceEEEeccCCHHHHHHHHHHHHHHHHH-cCCCC
Q 029591 66 ASGKMVCTGAKSEQQSKLAARKYARIIQK-LGFPA 99 (191)
Q Consensus 66 ~SGKivitGaks~e~a~~a~~~i~~~l~~-~g~~~ 99 (191)
=||.+++|| +..+.+.|++.+.+-+++ +||.+
T Consensus 73 FsGslvitG--dvs~Ve~Al~~V~~~l~~~L~F~~ 105 (111)
T PRK15468 73 FSGALVIYG--SVGAVEEALSQTVSGLGRLLNYTL 105 (111)
T ss_pred cceeEEEEc--cHHHHHHHHHHHHHHHHhhcCccc
Confidence 499999999 688999999999999998 78863
No 35
>cd03065 PDI_b_Calsequestrin_N PDIb family, Calsequestrin subfamily, N-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2
Probab=67.94 E-value=11 Score=28.75 Aligned_cols=29 Identities=14% Similarity=0.226 Sum_probs=23.7
Q ss_pred EEEEeecce-EEEeccCCHHHHHHHHHHHH
Q 029591 152 VLLIFVSGK-IVITGAKVRDETYTAFENIY 180 (191)
Q Consensus 152 t~lIF~sGk-ivitGaks~~~~~~a~~~i~ 180 (191)
|+++|.+|+ +-..|+++.+++.+.++++.
T Consensus 90 Tl~lfk~G~~v~~~G~~~~~~l~~~l~~~~ 119 (120)
T cd03065 90 SIYVFKDDEVIEYDGEFAADTLVEFLLDLI 119 (120)
T ss_pred EEEEEECCEEEEeeCCCCHHHHHHHHHHHh
Confidence 678999998 55779999998888877653
No 36
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=60.16 E-value=30 Score=30.88 Aligned_cols=35 Identities=20% Similarity=0.405 Sum_probs=28.3
Q ss_pred EecCCeEEEEEeecceEEEeccCCHHHHHHHHHHH
Q 029591 145 RMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENI 179 (191)
Q Consensus 145 r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~~i 179 (191)
+++.+.-.+..|++|+++|-|.+++.+++.-+.+.
T Consensus 303 ~vr~~~~~~~~~~~gr~~i~g~~~~~~a~~~~~~~ 337 (339)
T PRK07688 303 SFSLEEKRLVLFKDGRVLVHGTKDISEAKTIYHRY 337 (339)
T ss_pred EEecCCeEEEEEcCCCEEEECCCCHHHHHHHHHHh
Confidence 33344478899999999999999999988877654
No 37
>cd02965 HyaE HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the sole energy source. The E. coli HyaE protein is a chaperone that specifically interacts with the twin-arginine translocation (Tat) signal peptide of the [NiFe] hydrogenase-1 beta subunit precursor. Tat signal peptides target precursor proteins to the Tat protein export system, which facilitates the transport of fully folded proteins across the inner membrane. HyaE may be involved in regulating the traffic of [NiFe] hydrogenase-1 on the Tat transport pathway.
Probab=57.83 E-value=9.6 Score=28.88 Aligned_cols=52 Identities=21% Similarity=0.231 Sum_probs=32.2
Q ss_pred hhHHHHhcCC---ccccccCCCceeE--EEecCCeEEEEEeecceEE--EeccCCHHHHH
Q 029591 121 LEGLAYSHGA---FSSYEPELFPGLI--YRMKQPKIVLLIFVSGKIV--ITGAKVRDETY 173 (191)
Q Consensus 121 L~~la~~~~~---~~~YePe~fpgli--~r~~~~~~t~lIF~sGkiv--itGaks~~~~~ 173 (191)
|++++.+++. .+..+-+..|.+. |++..- -|+++|.+|+++ +.|..+.+++.
T Consensus 51 leela~e~~~~v~f~kVdid~~~~la~~f~V~sI-PTli~fkdGk~v~~~~G~~~~~e~~ 109 (111)
T cd02965 51 LPELLKAFPGRFRAAVVGRADEQALAARFGVLRT-PALLFFRDGRYVGVLAGIRDWDEYV 109 (111)
T ss_pred HHHHHHHCCCcEEEEEEECCCCHHHHHHcCCCcC-CEEEEEECCEEEEEEeCccCHHHHh
Confidence 5566666542 2244555555553 444321 278999999997 56988887654
No 38
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=53.84 E-value=23 Score=27.98 Aligned_cols=40 Identities=30% Similarity=0.497 Sum_probs=28.3
Q ss_pred EEecCCeEEEEEeecceEEE---ec--------cCCHHHHHHHHHHHHHHH
Q 029591 144 YRMKQPKIVLLIFVSGKIVI---TG--------AKVRDETYTAFENIYPVL 183 (191)
Q Consensus 144 ~r~~~~~~t~lIF~sGkivi---tG--------aks~~~~~~a~~~i~~~L 183 (191)
|.+.++-.++.+|.+|++.+ || ..+.+++.+.++.+++.-
T Consensus 73 y~I~~~~t~~~ffk~g~~~vd~~tG~~~k~~~~~~~k~~l~~~i~~~~~~a 123 (142)
T PLN00410 73 YELYDPCTVMFFFRNKHIMIDLGTGNNNKINWALKDKQEFIDIVETVYRGA 123 (142)
T ss_pred cCccCCCcEEEEEECCeEEEEEecccccccccccCCHHHHHHHHHHHHHHH
Confidence 44554545667999999655 77 567788888888777653
No 39
>cd03065 PDI_b_Calsequestrin_N PDIb family, Calsequestrin subfamily, N-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2
Probab=52.80 E-value=23 Score=26.97 Aligned_cols=29 Identities=7% Similarity=0.069 Sum_probs=22.3
Q ss_pred eEEEEecCce-EEEeccCCHHHHHHHHHHH
Q 029591 60 TTALIFASGK-MVCTGAKSEQQSKLAARKY 88 (191)
Q Consensus 60 ~t~lIf~SGK-ivitGaks~e~a~~a~~~i 88 (191)
-|+.+|.+|+ +-.+|+.+.++....++++
T Consensus 89 PTl~lfk~G~~v~~~G~~~~~~l~~~l~~~ 118 (120)
T cd03065 89 DSIYVFKDDEVIEYDGEFAADTLVEFLLDL 118 (120)
T ss_pred cEEEEEECCEEEEeeCCCCHHHHHHHHHHH
Confidence 4899999999 4455988888777766654
No 40
>PHA02278 thioredoxin-like protein
Probab=51.64 E-value=23 Score=26.01 Aligned_cols=23 Identities=17% Similarity=0.234 Sum_probs=19.4
Q ss_pred EEEEeecceEE--EeccCCHHHHHH
Q 029591 152 VLLIFVSGKIV--ITGAKVRDETYT 174 (191)
Q Consensus 152 t~lIF~sGkiv--itGaks~~~~~~ 174 (191)
|+++|..|+.+ +.|..+.+++.+
T Consensus 75 T~i~fk~G~~v~~~~G~~~~~~l~~ 99 (103)
T PHA02278 75 VLIGYKDGQLVKKYEDQVTPMQLQE 99 (103)
T ss_pred EEEEEECCEEEEEEeCCCCHHHHHh
Confidence 68999999999 999888877654
No 41
>KOG4749 consensus Inositol polyphosphate kinase [Signal transduction mechanisms]
Probab=51.54 E-value=4.2 Score=36.70 Aligned_cols=57 Identities=32% Similarity=0.525 Sum_probs=44.2
Q ss_pred cCCcccccc-CCCceeEEEec--------CCeEEEEEeecceEEEeccC-----CHHHHHHHHHHHHHHHH
Q 029591 128 HGAFSSYEP-ELFPGLIYRMK--------QPKIVLLIFVSGKIVITGAK-----VRDETYTAFENIYPVLT 184 (191)
Q Consensus 128 ~~~~~~YeP-e~fpgli~r~~--------~~~~t~lIF~sGkivitGak-----s~~~~~~a~~~i~~~L~ 184 (191)
+.+-++|+| ++|.|=.-||. .|.=-+-||.+|..|.-|.+ +..++..|++.+...+.
T Consensus 172 ~sqisey~PLDLfSG~k~rm~~AikaL~~~pqnnlrvF~nG~lv~gg~~~g~~kt~s~i~~~~~~~~k~~l 242 (375)
T KOG4749|consen 172 ISQISEYDPLDLFSGSKERMHKAIKALYSTPQNNLRVFLNGSLVFGGLGGGICKTTSEIELAFEDALKDFL 242 (375)
T ss_pred hhhhhccCchhhccccHHHHHHHHHHHhhccccceeEEeccceeecccCCCcccchhhhhHHHHHHHHHHh
Confidence 345689999 99999888873 46667899999999998854 55778888887766543
No 42
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=51.47 E-value=33 Score=27.06 Aligned_cols=62 Identities=19% Similarity=0.226 Sum_probs=36.3
Q ss_pred HHHHHhhCCC-ce---ecCCCCceE--EEEecCCceEEEEecCceEEE---ec--------cCCHHHHHHHHHHHHHHH
Q 029591 31 LKKIALQARN-AE---YNPKRFAAV--IMRIREPKTTALIFASGKMVC---TG--------AKSEQQSKLAARKYARII 92 (191)
Q Consensus 31 L~~la~~~~n-~e---YePe~fpgl--v~R~~~P~~t~lIf~SGKivi---tG--------aks~e~a~~a~~~i~~~l 92 (191)
|+++|..+++ +. =|=+..|.+ .+.+++|-+++.+|++|++.+ +| ..+.++....++.+.+--
T Consensus 45 l~~la~~~~~~~~~~kVDVDe~~dla~~y~I~~~~t~~~ffk~g~~~vd~~tG~~~k~~~~~~~k~~l~~~i~~~~~~a 123 (142)
T PLN00410 45 LASVAETIKNFAVIYLVDITEVPDFNTMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWALKDKQEFIDIVETVYRGA 123 (142)
T ss_pred HHHHHHHcCCceEEEEEECCCCHHHHHHcCccCCCcEEEEEECCeEEEEEecccccccccccCCHHHHHHHHHHHHHHH
Confidence 5677777655 22 233333333 345555656777999999443 55 456666666666665543
No 43
>KOG0910 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=51.05 E-value=27 Score=28.04 Aligned_cols=76 Identities=18% Similarity=0.211 Sum_probs=51.1
Q ss_pred ceeEEeEEEEEEcCCccC---hhHHHHhc-CC------ccccccCCCceeEEEecCCeEEEEEeecceEE--EeccCCHH
Q 029591 103 DFKIQNIVGSCDVKFPIR---LEGLAYSH-GA------FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV--ITGAKVRD 170 (191)
Q Consensus 103 ~~~i~Nivat~~l~~~i~---L~~la~~~-~~------~~~YePe~fpgli~r~~~~~~t~lIF~sGkiv--itGaks~~ 170 (191)
..-+.+.-|..+-|+.+= |++++.++ +. ++.=+||+ ...|.++-- -|+++|.+|..+ +.|+-..+
T Consensus 62 ~PVlVdF~A~WCgPCk~l~P~l~~~~~~~~g~~k~~kvdtD~~~el--a~~Y~I~av-PtvlvfknGe~~d~~vG~~~~~ 138 (150)
T KOG0910|consen 62 VPVLVDFHAEWCGPCKMLGPILEELVSEYAGKFKLYKVDTDEHPEL--AEDYEISAV-PTVLVFKNGEKVDRFVGAVPKE 138 (150)
T ss_pred CCEEEEEecCcCccHhHhhHHHHHHHHhhcCeEEEEEEccccccch--Hhhcceeee-eEEEEEECCEEeeeecccCCHH
Confidence 345677889988888664 55665543 11 23333333 334554421 368999999987 99999999
Q ss_pred HHHHHHHHHHH
Q 029591 171 ETYTAFENIYP 181 (191)
Q Consensus 171 ~~~~a~~~i~~ 181 (191)
.+.+.+++..+
T Consensus 139 ~l~~~i~k~l~ 149 (150)
T KOG0910|consen 139 QLRSLIKKFLK 149 (150)
T ss_pred HHHHHHHHHhc
Confidence 99999988764
No 44
>PF06277 EutA: Ethanolamine utilisation protein EutA; InterPro: IPR009377 Proteins in this entry are EutA ethanolamine utilization proteins, reactivating factors for ethanolamine ammonia lyase, encoded by the ethanolamine utilization eut operon. The holoenzyme of adenosylcobalamin-dependent ethanolamine ammonia-lyase (EutBC, IPR0092462 from INTERPRO, IPR010628 from INTERPRO), which is part of the ethanolamine utilization pathway [, , ], undergoes suicidal inactivation during catalysis as well as inactivation in the absence of substrate. The inactivation involves the irreversible cleavage of the Co-C bond of the coenzyme. The inactivated holoenzyme undergoes rapid and continuous reactivation in the presence of ATP, Mg2+, and free adenosylcobalamin in permeabilised cells (in situ), homogenate, and cell extracts of Escherichia coli. The EutA protein is essential for reactivation. It was demonstrated with purified recombinant EutA that both the suicidally inactivated and O2-inactivated holoethanolamine ammonia lyase underwent rapid reactivation in vitro by EutA in the presence of adenosylcobalamin, ATP, and Mg2+ []. The inactive enzyme-cyanocobalamin complex was also activated in situ and in vitro by EutA under the same conditions. Thus EutA is believed to be the only component of the reactivating factor for ethanolamine ammonia lyase. Reactivation and activation occur through the exchange of modified coenzyme for free intact adenosylcobalamin []. Bacteria that harbor the ethanolamine utilization pathway can use ethanolamine as a source of carbon and nitrogen. For more information on the ethanolamine utilization pathway, please see IPR009194 from INTERPRO, IPR012408 from INTERPRO.
Probab=50.83 E-value=89 Score=29.60 Aligned_cols=85 Identities=18% Similarity=0.278 Sum_probs=54.1
Q ss_pred cCceEEEeccCCHHHHHHHHHHHHHHHHHcCCCCcccceeEEeEEEEEEcCCccChhHHHHhcCCc-cccccCCCceeEE
Q 029591 66 ASGKMVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF-SSYEPELFPGLIY 144 (191)
Q Consensus 66 ~SGKivitGaks~e~a~~a~~~i~~~l~~~g~~~~~~~~~i~Nivat~~l~~~i~L~~la~~~~~~-~~YePe~fpgli~ 144 (191)
.+|-+++||-. .-++=++.+...|...--+ | +|||+- =|||.+-...|.. ..|.-+. ...+.
T Consensus 84 ~TGAVIITGET---ArKeNA~~v~~~Ls~~aGD-----F----VVATAG----PdLEsiiAgkGsGA~~~S~~~-~~~V~ 146 (473)
T PF06277_consen 84 DTGAVIITGET---ARKENAREVLHALSGFAGD-----F----VVATAG----PDLESIIAGKGSGAAALSKEH-HTVVA 146 (473)
T ss_pred ccccEEEecch---hhhhhHHHHHHHHHHhcCC-----E----EEEccC----CCHHHHHhccCccHHHHhhhh-CCeEE
Confidence 68999999932 2233334454445544222 2 678887 2999997766654 3555443 44444
Q ss_pred E--ecCCeEEEEEeecceEEEeccC
Q 029591 145 R--MKQPKIVLLIFVSGKIVITGAK 167 (191)
Q Consensus 145 r--~~~~~~t~lIF~sGkivitGak 167 (191)
. +-+-..-+.+|..|+++=|+|=
T Consensus 147 NiDIGGGTtN~avf~~G~v~~T~cl 171 (473)
T PF06277_consen 147 NIDIGGGTTNIAVFDNGEVIDTACL 171 (473)
T ss_pred EEEeCCCceeEEEEECCEEEEEEEE
Confidence 4 4456677899999999999863
No 45
>PRK09381 trxA thioredoxin; Provisional
Probab=50.59 E-value=24 Score=25.10 Aligned_cols=27 Identities=22% Similarity=0.397 Sum_probs=20.4
Q ss_pred EEEeecceEE--EeccCCHHHHHHHHHHH
Q 029591 153 LLIFVSGKIV--ITGAKVRDETYTAFENI 179 (191)
Q Consensus 153 ~lIF~sGkiv--itGaks~~~~~~a~~~i 179 (191)
+.+|..|+++ .+|..+.+++...++..
T Consensus 79 ~~~~~~G~~~~~~~G~~~~~~l~~~i~~~ 107 (109)
T PRK09381 79 LLLFKNGEVAATKVGALSKGQLKEFLDAN 107 (109)
T ss_pred EEEEeCCeEEEEecCCCCHHHHHHHHHHh
Confidence 5677888877 67888888887777643
No 46
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=50.56 E-value=34 Score=25.12 Aligned_cols=34 Identities=18% Similarity=0.270 Sum_probs=27.8
Q ss_pred ecCceEEEeccCCHHHHHHHHHHHHHHHHHcCCCC
Q 029591 65 FASGKMVCTGAKSEQQSKLAARKYARIIQKLGFPA 99 (191)
Q Consensus 65 f~SGKivitGaks~e~a~~a~~~i~~~l~~~g~~~ 99 (191)
+..-=|+||| .|..+.+..++.+.+.+++.|..+
T Consensus 28 ~~dy~VI~Tg-~S~rh~~aia~~v~~~~k~~~~~~ 61 (99)
T TIGR00090 28 IADYFVIASG-TSSRHVKAIADNVEEELKEAGLKP 61 (99)
T ss_pred ccCEEEEEEe-CCHHHHHHHHHHHHHHHHHcCCCc
Confidence 3355688888 789999999999999999888753
No 47
>PRK10996 thioredoxin 2; Provisional
Probab=49.19 E-value=27 Score=26.74 Aligned_cols=28 Identities=21% Similarity=0.441 Sum_probs=21.6
Q ss_pred EEEEeecceEE--EeccCCHHHHHHHHHHH
Q 029591 152 VLLIFVSGKIV--ITGAKVRDETYTAFENI 179 (191)
Q Consensus 152 t~lIF~sGkiv--itGaks~~~~~~a~~~i 179 (191)
++++|.+|+++ +.|..+.+++.+.++++
T Consensus 109 tlii~~~G~~v~~~~G~~~~e~l~~~l~~~ 138 (139)
T PRK10996 109 TIMIFKNGQVVDMLNGAVPKAPFDSWLNEA 138 (139)
T ss_pred EEEEEECCEEEEEEcCCCCHHHHHHHHHHh
Confidence 35678888887 67888888888877754
No 48
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=47.25 E-value=62 Score=25.91 Aligned_cols=51 Identities=16% Similarity=0.275 Sum_probs=37.3
Q ss_pred CceEEEEecCCceEEE-EecCceEEEeccCC---HHHHHHHHHHHHHHHHHcCCC
Q 029591 48 FAAVIMRIREPKTTAL-IFASGKMVCTGAKS---EQQSKLAARKYARIIQKLGFP 98 (191)
Q Consensus 48 fpglv~R~~~P~~t~l-If~SGKivitGaks---~e~a~~a~~~i~~~l~~~g~~ 98 (191)
|+--++-+.|..-.++ +.++|.+-..|.+. .=.|..|++.+++...++|+.
T Consensus 37 ~NNTiItiTD~~G~~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~ 91 (149)
T PTZ00129 37 FNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGIN 91 (149)
T ss_pred cCCeEEEEEcccCCEEEEEecCcceecccccCCCHHHHHHHHHHHHHHHHHcCCe
Confidence 4445566666654444 45789999999873 337888899999999999885
No 49
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=44.79 E-value=19 Score=24.03 Aligned_cols=22 Identities=23% Similarity=0.418 Sum_probs=17.9
Q ss_pred cceEEEeccCCHHHHHHHHHHH
Q 029591 158 SGKIVITGAKVRDETYTAFENI 179 (191)
Q Consensus 158 sGkivitGaks~~~~~~a~~~i 179 (191)
.|+..+.|..+.+++.+.++..
T Consensus 60 ~g~~~~~G~~~~~~l~~~l~~~ 81 (82)
T TIGR00411 60 NGDVEFIGAPTKEELVEAIKKR 81 (82)
T ss_pred CCEEEEecCCCHHHHHHHHHhh
Confidence 6778899999999888877653
No 50
>cd02948 TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which
Probab=44.76 E-value=34 Score=24.41 Aligned_cols=26 Identities=23% Similarity=0.406 Sum_probs=19.3
Q ss_pred EEEEeecceEE--EeccCCHHHHHHHHHH
Q 029591 152 VLLIFVSGKIV--ITGAKVRDETYTAFEN 178 (191)
Q Consensus 152 t~lIF~sGkiv--itGaks~~~~~~a~~~ 178 (191)
|+++|.+|+.+ +.|+ +.+++.++++.
T Consensus 74 t~~~~~~g~~~~~~~G~-~~~~~~~~i~~ 101 (102)
T cd02948 74 TFLFYKNGELVAVIRGA-NAPLLNKTITE 101 (102)
T ss_pred EEEEEECCEEEEEEecC-ChHHHHHHHhh
Confidence 46888899876 7776 66778877764
No 51
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=43.93 E-value=1.9e+02 Score=25.29 Aligned_cols=93 Identities=8% Similarity=0.035 Sum_probs=48.6
Q ss_pred EEEeccCCHHHHHHHHHHHHHHHHHcCCCCccccee------EEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeE
Q 029591 70 MVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFK------IQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLI 143 (191)
Q Consensus 70 ivitGaks~e~a~~a~~~i~~~l~~~g~~~~~~~~~------i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli 143 (191)
+.+.|..+.. + +.++.+.|.+.|+.+.-.+-. .=.+.+.++++-..+++.|...+.. .-.++ ++.
T Consensus 10 itv~G~DrpG-I---Va~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~p~~~~~~~L~~~L~~---l~~~l--~l~ 80 (286)
T PRK13011 10 LTLSCPSAAG-I---VAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSEEGLDEDALRAGFAP---IAARF--GMQ 80 (286)
T ss_pred EEEEeCCCCC-H---HHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecCCCCCHHHHHHHHHH---HHHHh--CcE
Confidence 4555644432 2 335566688888764221111 1135666777777777776654311 11122 223
Q ss_pred EEe--cCCeEEEEEeecceEEEeccCCHHHHHHHH
Q 029591 144 YRM--KQPKIVLLIFVSGKIVITGAKVRDETYTAF 176 (191)
Q Consensus 144 ~r~--~~~~~t~lIF~sGkivitGaks~~~~~~a~ 176 (191)
.++ ..++.++.||.||. +.+.+.+.+++
T Consensus 81 i~i~~~~~~~ri~vl~Sg~-----g~nl~al~~~~ 110 (286)
T PRK13011 81 WELHDPAARPKVLIMVSKF-----DHCLNDLLYRW 110 (286)
T ss_pred EEEeecccCceEEEEEcCC-----cccHHHHHHHH
Confidence 332 34556789999993 55555555544
No 52
>PRK09381 trxA thioredoxin; Provisional
Probab=43.05 E-value=36 Score=24.17 Aligned_cols=28 Identities=32% Similarity=0.323 Sum_probs=21.1
Q ss_pred EEEEecCceEE--EeccCCHHHHHHHHHHH
Q 029591 61 TALIFASGKMV--CTGAKSEQQSKLAARKY 88 (191)
Q Consensus 61 t~lIf~SGKiv--itGaks~e~a~~a~~~i 88 (191)
++.+|.+|+++ .+|..+.++.+..++..
T Consensus 78 t~~~~~~G~~~~~~~G~~~~~~l~~~i~~~ 107 (109)
T PRK09381 78 TLLLFKNGEVAATKVGALSKGQLKEFLDAN 107 (109)
T ss_pred EEEEEeCCeEEEEecCCCCHHHHHHHHHHh
Confidence 78888999988 66888877766665543
No 53
>cd02963 TRX_DnaJ TRX domain, DnaJ domain containing protein family; composed of uncharacterized proteins of about 500-800 amino acids, containing an N-terminal DnaJ domain followed by one redox active TRX domain. DnaJ is a member of the 40 kDa heat-shock protein (Hsp40) family of molecular chaperones, which regulate the activity of Hsp70s. TRX is involved in the redox regulation of many protein substrates through the reduction of disulfide bonds. TRX has been implicated to catalyse the reduction of Hsp33, a chaperone holdase that binds to unfolded protein intermediates. The presence of DnaJ and TRX domains in members of this family suggests that they could be involved in a redox-regulated chaperone network.
Probab=42.61 E-value=31 Score=25.08 Aligned_cols=26 Identities=4% Similarity=0.184 Sum_probs=18.6
Q ss_pred EEEeecceEE--EeccCCHHHHHHHHHH
Q 029591 153 LLIFVSGKIV--ITGAKVRDETYTAFEN 178 (191)
Q Consensus 153 ~lIF~sGkiv--itGaks~~~~~~a~~~ 178 (191)
+.+|..|+++ ..|..+.+++.+.+++
T Consensus 83 ~~i~~~g~~~~~~~G~~~~~~l~~~i~~ 110 (111)
T cd02963 83 IVGIINGQVTFYHDSSFTKQHVVDFVRK 110 (111)
T ss_pred EEEEECCEEEEEecCCCCHHHHHHHHhc
Confidence 5677788877 4587888877776654
No 54
>PF07338 DUF1471: Protein of unknown function (DUF1471); InterPro: IPR010854 This entry consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some of the proteins are annotated as ydgH precursors and contain two copies of this region, one at the N terminus and the other at the C terminus. The function of this family is unknown.; PDB: 2NOC_A 2JNA_B 4EVU_B.
Probab=42.51 E-value=32 Score=22.71 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=20.3
Q ss_pred ecceEEEecc-CCHHHHHHHHHHHH
Q 029591 157 VSGKIVITGA-KVRDETYTAFENIY 180 (191)
Q Consensus 157 ~sGkivitGa-ks~~~~~~a~~~i~ 180 (191)
+-|.|.++|. .+++|+.+++..-.
T Consensus 4 ~iG~Isvs~~~~s~~d~~~~la~kA 28 (56)
T PF07338_consen 4 KIGTISVSGNFGSPDDAEEALAKKA 28 (56)
T ss_dssp EEEEEEEEEECSSHHHHHHHHHHHH
T ss_pred EEEEEEEccccCCHHHHHHHHHHHH
Confidence 3589999999 99999999987644
No 55
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=40.95 E-value=1.1e+02 Score=23.29 Aligned_cols=50 Identities=14% Similarity=0.293 Sum_probs=36.5
Q ss_pred cCCCceeEEEecCCeEEEEEeecc-eEEEecc-----CCHHHHHHHHHHHHHHHHh
Q 029591 136 PELFPGLIYRMKQPKIVLLIFVSG-KIVITGA-----KVRDETYTAFENIYPVLTE 185 (191)
Q Consensus 136 Pe~fpgli~r~~~~~~t~lIF~sG-kivitGa-----ks~~~~~~a~~~i~~~L~~ 185 (191)
.+.|-|+++++.+-++...+=.|| |+++.-. ...++++.-++.++..-.+
T Consensus 49 ~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~~~~~~~~d~~ik~fF~~vh~~Y~~ 104 (132)
T PF04628_consen 49 SDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHDMSDNSIRDEDIKQFFKEVHELYVK 104 (132)
T ss_dssp SCSEEEEEEEETTEEEEEEETTT--EEEEEECGGG-S--HHHHHHHHHHHHHHHHH
T ss_pred cccccCceehhhhHHHHhhhccCceeEEEEEecccCCcchHHHHHHHHHHHHHHHH
Confidence 467889999999999988888888 6665543 5778888888888776444
No 56
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=40.94 E-value=76 Score=19.28 Aligned_cols=28 Identities=11% Similarity=0.158 Sum_probs=21.7
Q ss_pred CceEEEEecCceEEEeccCCHHHHHHHH
Q 029591 58 PKTTALIFASGKMVCTGAKSEQQSKLAA 85 (191)
Q Consensus 58 P~~t~lIf~SGKivitGaks~e~a~~a~ 85 (191)
....++||.+|++.+.-.=+.+.|+.-+
T Consensus 4 ~~~qLTIfY~G~V~Vfd~v~~~Ka~~im 31 (36)
T PF06200_consen 4 ETAQLTIFYGGQVCVFDDVPPDKAQEIM 31 (36)
T ss_pred CCCcEEEEECCEEEEeCCCCHHHHHHHH
Confidence 3467899999999999877777666544
No 57
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=38.36 E-value=75 Score=21.63 Aligned_cols=26 Identities=23% Similarity=0.434 Sum_probs=19.2
Q ss_pred EEEeecceEE--EeccCCHHHHHHHHHH
Q 029591 153 LLIFVSGKIV--ITGAKVRDETYTAFEN 178 (191)
Q Consensus 153 ~lIF~sGkiv--itGaks~~~~~~a~~~ 178 (191)
+++|.+|+.+ +.|..+.+++.+.+++
T Consensus 75 ~~~~~~g~~~~~~~g~~~~~~l~~~i~~ 102 (103)
T PF00085_consen 75 IIFFKNGKEVKRYNGPRNAESLIEFIEK 102 (103)
T ss_dssp EEEEETTEEEEEEESSSSHHHHHHHHHH
T ss_pred EEEEECCcEEEEEECCCCHHHHHHHHHc
Confidence 4566666665 7899999988887763
No 58
>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.
Probab=37.69 E-value=64 Score=23.47 Aligned_cols=30 Identities=20% Similarity=0.352 Sum_probs=23.7
Q ss_pred CceEEEeccCCHHHHHHHHHHHHHHH-HHcCC
Q 029591 67 SGKMVCTGAKSEQQSKLAARKYARII-QKLGF 97 (191)
Q Consensus 67 SGKivitGaks~e~a~~a~~~i~~~l-~~~g~ 97 (191)
.-=|++|| +|..+++..++.+.+.+ ++.|.
T Consensus 30 dy~II~T~-~S~rh~~aia~~v~~~~~k~~~~ 60 (100)
T PF02410_consen 30 DYFIIATG-RSERHVRAIADEVEKALKKEYGE 60 (100)
T ss_dssp SEEEEEEE-SSHHHHHHHHHHHHHHH-HHTT-
T ss_pred CEEEEEEc-CCHHHHHHHHHHHHHHHHHHcCC
Confidence 44578888 78999999999999999 55553
No 59
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=37.25 E-value=2.8e+02 Score=24.15 Aligned_cols=94 Identities=11% Similarity=0.050 Sum_probs=50.5
Q ss_pred EEEeccCCHHHHHHHHHHHHHHHHHcCCCCccccee------EEeEEEEEEc-CCccChhHHHHhcCCccccccCCCcee
Q 029591 70 MVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFK------IQNIVGSCDV-KFPIRLEGLAYSHGAFSSYEPELFPGL 142 (191)
Q Consensus 70 ivitGaks~e~a~~a~~~i~~~l~~~g~~~~~~~~~------i~Nivat~~l-~~~i~L~~la~~~~~~~~YePe~fpgl 142 (191)
+.+.|..+. .. +.++.+.|.+.|+.+.-.+.. .=.+...+++ +.+.+++.|...+. ....++ ++
T Consensus 9 itv~G~Drp-GI---Va~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~~~~~~~~~L~~~L~---~l~~~l--~l 79 (286)
T PRK06027 9 LTLSCPDRP-GI---VAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDGLIFNLETLRADFA---ALAEEF--EM 79 (286)
T ss_pred EEEECCCCC-cH---HHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCCCCCCHHHHHHHHH---HHHHHh--CC
Confidence 455564443 22 235566688888765222111 1234555666 55667666665432 111122 34
Q ss_pred EEEec--CCeEEEEEeecceEEEeccCCHHHHHHHHH
Q 029591 143 IYRMK--QPKIVLLIFVSGKIVITGAKVRDETYTAFE 177 (191)
Q Consensus 143 i~r~~--~~~~t~lIF~sGkivitGaks~~~~~~a~~ 177 (191)
...+. .++.++.||.||. +.+.+.+.++++
T Consensus 80 ~i~l~~~~~~~ri~vl~Sg~-----gsnl~al~~~~~ 111 (286)
T PRK06027 80 DWRLLDSAERKRVVILVSKE-----DHCLGDLLWRWR 111 (286)
T ss_pred EEEEcccccCcEEEEEEcCC-----CCCHHHHHHHHH
Confidence 44433 3557889999998 556666665543
No 60
>cd07047 BMC_PduB_repeat1 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 1. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduB).
Probab=37.21 E-value=59 Score=25.53 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=23.2
Q ss_pred cceEEEeccCCHHHHHHHHHHHHHHHHhh
Q 029591 158 SGKIVITGAKVRDETYTAFENIYPVLTEF 186 (191)
Q Consensus 158 sGkivitGaks~~~~~~a~~~i~~~L~~~ 186 (191)
.|.+++||+-+..+++.|++.-...+.++
T Consensus 78 kg~vvitGg~dVs~V~~aVeaa~~~v~~~ 106 (134)
T cd07047 78 HGSLILFGAEDVSDVRRAVEVALSETEKT 106 (134)
T ss_pred eEEEEEEcCCCHHHHHHHHHHHHHHHHHh
Confidence 78899999999999877777766665554
No 61
>KOG0910 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=36.94 E-value=57 Score=26.14 Aligned_cols=30 Identities=30% Similarity=0.511 Sum_probs=26.4
Q ss_pred eEEEEecCceEE--EeccCCHHHHHHHHHHHH
Q 029591 60 TTALIFASGKMV--CTGAKSEQQSKLAARKYA 89 (191)
Q Consensus 60 ~t~lIf~SGKiv--itGaks~e~a~~a~~~i~ 89 (191)
-|+++|.+|.-+ +.|+...+.....++++.
T Consensus 117 PtvlvfknGe~~d~~vG~~~~~~l~~~i~k~l 148 (150)
T KOG0910|consen 117 PTVLVFKNGEKVDRFVGAVPKEQLRSLIKKFL 148 (150)
T ss_pred eEEEEEECCEEeeeecccCCHHHHHHHHHHHh
Confidence 489999999987 889999999999888875
No 62
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=36.76 E-value=43 Score=22.72 Aligned_cols=22 Identities=27% Similarity=0.552 Sum_probs=16.1
Q ss_pred eecceEEEec-cCCHHHHHHHHH
Q 029591 156 FVSGKIVITG-AKVRDETYTAFE 177 (191)
Q Consensus 156 F~sGkivitG-aks~~~~~~a~~ 177 (191)
+-+|++...| .-+.+++...++
T Consensus 54 vIng~~~~~G~~p~~~el~~~l~ 76 (76)
T PF13192_consen 54 VINGKVVFVGRVPSKEELKELLE 76 (76)
T ss_dssp EETTEEEEESS--HHHHHHHHHH
T ss_pred EECCEEEEEecCCCHHHHHHHhC
Confidence 4479999999 888888887654
No 63
>PHA02278 thioredoxin-like protein
Probab=36.03 E-value=52 Score=24.08 Aligned_cols=24 Identities=13% Similarity=0.191 Sum_probs=19.1
Q ss_pred eEEEEecCceEE--EeccCCHHHHHH
Q 029591 60 TTALIFASGKMV--CTGAKSEQQSKL 83 (191)
Q Consensus 60 ~t~lIf~SGKiv--itGaks~e~a~~ 83 (191)
.|+.+|++|+.+ +.|..+.++..+
T Consensus 74 PT~i~fk~G~~v~~~~G~~~~~~l~~ 99 (103)
T PHA02278 74 PVLIGYKDGQLVKKYEDQVTPMQLQE 99 (103)
T ss_pred cEEEEEECCEEEEEEeCCCCHHHHHh
Confidence 389999999999 888777766543
No 64
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=35.51 E-value=74 Score=24.79 Aligned_cols=30 Identities=17% Similarity=0.215 Sum_probs=24.0
Q ss_pred eEEEEecCceEE--EeccCCHHHHHHHHHHHH
Q 029591 60 TTALIFASGKMV--CTGAKSEQQSKLAARKYA 89 (191)
Q Consensus 60 ~t~lIf~SGKiv--itGaks~e~a~~a~~~i~ 89 (191)
-|+++|++|+.+ +.|..+.++...-+++++
T Consensus 93 PTLl~FkdGk~v~~i~G~~~k~~l~~~I~~~L 124 (132)
T PRK11509 93 PATLVFTGGNYRGVLNGIHPWAELINLMRGLV 124 (132)
T ss_pred CEEEEEECCEEEEEEeCcCCHHHHHHHHHHHh
Confidence 399999999997 679989888877666553
No 65
>cd02950 TxlA TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport.
Probab=34.92 E-value=74 Score=24.41 Aligned_cols=28 Identities=7% Similarity=0.175 Sum_probs=21.3
Q ss_pred EEEe-ecceEE--EeccCCHHHHHHHHHHHH
Q 029591 153 LLIF-VSGKIV--ITGAKVRDETYTAFENIY 180 (191)
Q Consensus 153 ~lIF-~sGkiv--itGaks~~~~~~a~~~i~ 180 (191)
+.+| .+|+++ +.|....+++.+.++.++
T Consensus 80 ~v~~~~~G~~v~~~~G~~~~~~l~~~l~~l~ 110 (142)
T cd02950 80 FVFLDREGNEEGQSIGLQPKQVLAQNLDALV 110 (142)
T ss_pred EEEECCCCCEEEEEeCCCCHHHHHHHHHHHH
Confidence 4566 478887 789999888888877655
No 66
>PRK11538 ribosome-associated protein; Provisional
Probab=34.30 E-value=85 Score=23.38 Aligned_cols=33 Identities=18% Similarity=0.302 Sum_probs=26.5
Q ss_pred ecCceEEEeccCCHHHHHHHHHHHHHHHHHcCCC
Q 029591 65 FASGKMVCTGAKSEQQSKLAARKYARIIQKLGFP 98 (191)
Q Consensus 65 f~SGKivitGaks~e~a~~a~~~i~~~l~~~g~~ 98 (191)
+...=|++|| .|..+++..++.+.+.+++.|..
T Consensus 33 ~~Dy~VIatg-~S~rh~~aia~~v~~~~k~~~~~ 65 (105)
T PRK11538 33 ITDCMIICTG-TSSRHVMSIADHVVQESRAAGLL 65 (105)
T ss_pred ccCEEEEEEe-CCHHHHHHHHHHHHHHHHHcCCC
Confidence 3456678887 68899999999999999887764
No 67
>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.
Probab=33.66 E-value=55 Score=27.19 Aligned_cols=28 Identities=14% Similarity=0.256 Sum_probs=24.6
Q ss_pred EeccCCHHHHHHHHHHHHHHHHHcCCCC
Q 029591 72 CTGAKSEQQSKLAARKYARIIQKLGFPA 99 (191)
Q Consensus 72 itGaks~e~a~~a~~~i~~~l~~~g~~~ 99 (191)
+.|+.+++++...++++.++|++.|++.
T Consensus 145 li~~~s~~e~~~~~~~v~~~L~~~Gf~l 172 (213)
T cd01644 145 LVSTDTLNEAVNVAKRLIALLKKGGFNL 172 (213)
T ss_pred eecCCCHHHHHHHHHHHHHHHHhCCccc
Confidence 3466899999999999999999999975
No 68
>cd02956 ybbN ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.
Probab=33.49 E-value=56 Score=22.45 Aligned_cols=25 Identities=20% Similarity=0.460 Sum_probs=17.7
Q ss_pred EEEEeecceEE--EeccCCHHHHHHHH
Q 029591 152 VLLIFVSGKIV--ITGAKVRDETYTAF 176 (191)
Q Consensus 152 t~lIF~sGkiv--itGaks~~~~~~a~ 176 (191)
++.+|..|+.+ ..|..+.+++...+
T Consensus 69 t~~~~~~g~~~~~~~g~~~~~~l~~~l 95 (96)
T cd02956 69 TVYLFAAGQPVDGFQGAQPEEQLRQML 95 (96)
T ss_pred EEEEEeCCEEeeeecCCCCHHHHHHHh
Confidence 35667778775 77888888776644
No 69
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=33.38 E-value=50 Score=25.14 Aligned_cols=31 Identities=26% Similarity=0.214 Sum_probs=23.5
Q ss_pred EEEeecceEEEeccCCHHHHHHHHHHHHHHHHh
Q 029591 153 LLIFVSGKIVITGAKVRDETYTAFENIYPVLTE 185 (191)
Q Consensus 153 ~lIF~sGkivitGaks~~~~~~a~~~i~~~L~~ 185 (191)
++==-||.+++||.-+ +++.|++.+...|.+
T Consensus 69 F~DRFsGslvitGdvs--~Ve~Al~~V~~~l~~ 99 (111)
T PRK15468 69 FLDRFSGALVIYGSVG--AVEEALSQTVSGLGR 99 (111)
T ss_pred eeeccceeEEEEccHH--HHHHHHHHHHHHHHh
Confidence 4444589999999765 588888888877765
No 70
>PF03135 CagE_TrbE_VirB: CagE, TrbE, VirB family, component of type IV transporter system; InterPro: IPR018145 This domain is found in (amongst others): the Helicobacter pylori protein CagE (see examples), which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration []. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro []. Similar type IV transport systems are also found in other bacteria. This domain is also found in proteins from the trb and Vir conjugal transfer systems in Agrobacterium tumefaciens and homologues of VirB proteins from other species.; GO: 0005524 ATP binding
Probab=33.33 E-value=60 Score=26.32 Aligned_cols=38 Identities=13% Similarity=0.182 Sum_probs=30.3
Q ss_pred EEEEecCceEEEeccCCHHHHHHHHHHHHHHHHHcCCCC
Q 029591 61 TALIFASGKMVCTGAKSEQQSKLAARKYARIIQKLGFPA 99 (191)
Q Consensus 61 t~lIf~SGKivitGaks~e~a~~a~~~i~~~l~~~g~~~ 99 (191)
...=+.+..|++.| +|.++++..++++.+.|...|+.+
T Consensus 144 ~~~G~~~~~i~v~~-~~~~~l~~~~~~v~~~l~~~G~~~ 181 (205)
T PF03135_consen 144 VSFGYYHFTIVVFA-DDPEELDDKVAEVSSALNNLGFVA 181 (205)
T ss_pred eeeeeeEEEEEEEc-CCHHHHHHHHHHHHHHHHHCCCEE
Confidence 34445566677776 899999999999999999999853
No 71
>cd02963 TRX_DnaJ TRX domain, DnaJ domain containing protein family; composed of uncharacterized proteins of about 500-800 amino acids, containing an N-terminal DnaJ domain followed by one redox active TRX domain. DnaJ is a member of the 40 kDa heat-shock protein (Hsp40) family of molecular chaperones, which regulate the activity of Hsp70s. TRX is involved in the redox regulation of many protein substrates through the reduction of disulfide bonds. TRX has been implicated to catalyse the reduction of Hsp33, a chaperone holdase that binds to unfolded protein intermediates. The presence of DnaJ and TRX domains in members of this family suggests that they could be involved in a redox-regulated chaperone network.
Probab=32.92 E-value=53 Score=23.84 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=19.7
Q ss_pred EEEEecCceEEE--eccCCHHHHHHHHHH
Q 029591 61 TALIFASGKMVC--TGAKSEQQSKLAARK 87 (191)
Q Consensus 61 t~lIf~SGKivi--tGaks~e~a~~a~~~ 87 (191)
|+.+|..|+++- .|..+.++....+++
T Consensus 82 t~~i~~~g~~~~~~~G~~~~~~l~~~i~~ 110 (111)
T cd02963 82 AIVGIINGQVTFYHDSSFTKQHVVDFVRK 110 (111)
T ss_pred EEEEEECCEEEEEecCCCCHHHHHHHHhc
Confidence 788899999984 477777766655543
No 72
>PRK10996 thioredoxin 2; Provisional
Probab=32.87 E-value=78 Score=24.12 Aligned_cols=28 Identities=25% Similarity=0.319 Sum_probs=21.5
Q ss_pred EEEEecCceEE--EeccCCHHHHHHHHHHH
Q 029591 61 TALIFASGKMV--CTGAKSEQQSKLAARKY 88 (191)
Q Consensus 61 t~lIf~SGKiv--itGaks~e~a~~a~~~i 88 (191)
++.+|.+|+++ ..|..+.++....+++.
T Consensus 109 tlii~~~G~~v~~~~G~~~~e~l~~~l~~~ 138 (139)
T PRK10996 109 TIMIFKNGQVVDMLNGAVPKAPFDSWLNEA 138 (139)
T ss_pred EEEEEECCEEEEEEcCCCCHHHHHHHHHHh
Confidence 67889999988 56888887777766543
No 73
>PF11869 DUF3389: Protein of unknown function (DUF3389); InterPro: IPR021811 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=31.87 E-value=24 Score=25.04 Aligned_cols=11 Identities=45% Similarity=0.754 Sum_probs=9.2
Q ss_pred EEeecceEEEe
Q 029591 154 LIFVSGKIVIT 164 (191)
Q Consensus 154 lIF~sGkivit 164 (191)
.=|+.|||+.|
T Consensus 3 I~Fs~GKiI~t 13 (75)
T PF11869_consen 3 IEFSQGKIIAT 13 (75)
T ss_pred EEecCCeEEEc
Confidence 34999999987
No 74
>COG0533 QRI7 Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=31.70 E-value=1.1e+02 Score=27.89 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=40.9
Q ss_pred CCceEEEEecCCceEEEEecC-ceEEEeccCCHHHHHHHHHHHHHHH
Q 029591 47 RFAAVIMRIREPKTTALIFAS-GKMVCTGAKSEQQSKLAARKYARII 92 (191)
Q Consensus 47 ~fpglv~R~~~P~~t~lIf~S-GKivitGaks~e~a~~a~~~i~~~l 92 (191)
.||.+.+-...-.+.+..+++ |++-+-|....+.+=+|.+|++|.|
T Consensus 125 ~~p~v~LlVSGGHTqli~~~~~g~y~ilGeTlDdA~Gea~DKvAR~l 171 (342)
T COG0533 125 AFPPVALLVSGGHTQLIAVRGIGRYEVLGETLDDAAGEAFDKVARLL 171 (342)
T ss_pred CCCcEEEEEecCceEEEEEcCCCcEEEEeeechhhhhHHHHHHHHHh
Confidence 899999999998999999999 9999999877777779999998764
No 75
>cd02949 TRX_NTR TRX domain, novel NADPH thioredoxin reductase (NTR) family; composed of fusion proteins found only in oxygenic photosynthetic organisms containing both TRX and NTR domains. The TRX domain functions as a protein disulfide reductase via the reversible oxidation of an active center dithiol present in a CXXC motif, while the NTR domain functions as a reductant to oxidized TRX. The fusion protein is bifunctional, showing both TRX and NTR activities, but it is not an independent NTR/TRX system. In plants, the protein is found exclusively in shoots and mature leaves and is localized in the chloroplast. It is involved in plant protection against oxidative stress.
Probab=31.57 E-value=68 Score=22.39 Aligned_cols=25 Identities=24% Similarity=0.428 Sum_probs=19.3
Q ss_pred EEEEeecceEE--EeccCCHHHHHHHH
Q 029591 152 VLLIFVSGKIV--ITGAKVRDETYTAF 176 (191)
Q Consensus 152 t~lIF~sGkiv--itGaks~~~~~~a~ 176 (191)
++.+|..|+++ +.|..+.+++.+.+
T Consensus 70 t~~i~~~g~~v~~~~g~~~~~~~~~~l 96 (97)
T cd02949 70 TVQFFKDKELVKEISGVKMKSEYREFI 96 (97)
T ss_pred EEEEEECCeEEEEEeCCccHHHHHHhh
Confidence 46788899998 78888888766654
No 76
>PRK10259 hypothetical protein; Provisional
Probab=30.71 E-value=60 Score=23.55 Aligned_cols=24 Identities=17% Similarity=0.129 Sum_probs=20.1
Q ss_pred ecceEEEeccCCHHHHHHHHHHHH
Q 029591 157 VSGKIVITGAKVRDETYTAFENIY 180 (191)
Q Consensus 157 ~sGkivitGaks~~~~~~a~~~i~ 180 (191)
.-|-|.++|..+++|+++.+..-.
T Consensus 36 kiG~VSvsg~~s~~d~~~~La~KA 59 (86)
T PRK10259 36 KIGVVSADGASTLDALEAKLAEKA 59 (86)
T ss_pred cceEEEEecCCCHHHHHHHHHHHH
Confidence 568999999999999999887543
No 77
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=30.44 E-value=1.6e+02 Score=21.69 Aligned_cols=32 Identities=16% Similarity=0.209 Sum_probs=24.9
Q ss_pred EEEeccCCHHHHHHHHHHHHHHHHH-cCCCCcc
Q 029591 70 MVCTGAKSEQQSKLAARKYARIIQK-LGFPAKF 101 (191)
Q Consensus 70 ivitGaks~e~a~~a~~~i~~~l~~-~g~~~~~ 101 (191)
|.+.|..+.|+-++-.+.+.+.|++ +|++++-
T Consensus 63 i~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~r 95 (116)
T PTZ00397 63 VTSIGGISRSNNSSIAAAITKILASHLKVKSER 95 (116)
T ss_pred EEEecCCCHHHHHHHHHHHHHHHHHHhCcCccc
Confidence 4445778888888888899999977 7997543
No 78
>PF06526 DUF1107: Protein of unknown function (DUF1107); InterPro: IPR009491 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2JRO_A.
Probab=29.78 E-value=86 Score=21.58 Aligned_cols=32 Identities=16% Similarity=0.323 Sum_probs=20.9
Q ss_pred EEecCceEEEeccCCHHHHHHHHHHHHHHHHHc
Q 029591 63 LIFASGKMVCTGAKSEQQSKLAARKYARIIQKL 95 (191)
Q Consensus 63 lIf~SGKivitGaks~e~a~~a~~~i~~~l~~~ 95 (191)
.=|.+||+....- +......++.++.+.+.++
T Consensus 32 feFd~Gkillp~~-~~~~~~~~~~EiN~~I~~L 63 (64)
T PF06526_consen 32 FEFDNGKILLPKK-ADKRHLSVMSEINQEIRRL 63 (64)
T ss_dssp EEEETTEE---SS---HHHHHHHHHHHHHHHHH
T ss_pred EEEcCCEEeCCcc-ccHHHHHHHHHHHHHHHhc
Confidence 3588999999874 5567778888888887764
No 79
>TIGR01068 thioredoxin thioredoxin. Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model.
Probab=29.05 E-value=1e+02 Score=20.83 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=16.6
Q ss_pred EEEeecceEE--EeccCCHHHHHHHHHH
Q 029591 153 LLIFVSGKIV--ITGAKVRDETYTAFEN 178 (191)
Q Consensus 153 ~lIF~sGkiv--itGaks~~~~~~a~~~ 178 (191)
+++|..|+.+ +.|..+.+++.+.++.
T Consensus 72 ~~~~~~g~~~~~~~g~~~~~~l~~~l~~ 99 (101)
T TIGR01068 72 LLLFKNGKEVDRSVGALPKAALKQLINK 99 (101)
T ss_pred EEEEeCCcEeeeecCCCCHHHHHHHHHh
Confidence 3445566653 5688887777776654
No 80
>TIGR00385 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily. Involved in the biogenesis of c-type cytochromes as well as in disulfide bond formation in some periplasmic proteins.
Probab=28.70 E-value=88 Score=24.55 Aligned_cols=48 Identities=17% Similarity=0.086 Sum_probs=32.1
Q ss_pred ccccCCCceeEEEecCCeEEEEEeecceEE--EeccCCHHHHHHHHHHHH
Q 029591 133 SYEPELFPGLIYRMKQPKIVLLIFVSGKIV--ITGAKVRDETYTAFENIY 180 (191)
Q Consensus 133 ~YePe~fpgli~r~~~~~~t~lIF~sGkiv--itGaks~~~~~~a~~~i~ 180 (191)
.+||..--+-.|.....-.+++|..+|+|+ .+|.-+.+++.+.++.++
T Consensus 122 ~~D~~~~~~~~~~v~~~P~~~~id~~G~i~~~~~G~~~~~~l~~~l~~~~ 171 (173)
T TIGR00385 122 LIDPNGKLGLDLGVYGAPETFLVDGNGVILYRHAGPLNNEVWTEGFLPAM 171 (173)
T ss_pred EECCCCchHHhcCCeeCCeEEEEcCCceEEEEEeccCCHHHHHHHHHHHh
Confidence 346554444445555544789999999987 458888888877766543
No 81
>COG3445 Acid-induced glycyl radical enzyme [General function prediction only]
Probab=28.45 E-value=24 Score=26.63 Aligned_cols=51 Identities=16% Similarity=0.154 Sum_probs=32.8
Q ss_pred CCccChhHHHHhcCCccccccCCCceeEEEecCCeEEEEEeecceEEEeccCCHHHHHHHHH
Q 029591 116 KFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFE 177 (191)
Q Consensus 116 ~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~~~~t~lIF~sGkivitGaks~~~~~~a~~ 177 (191)
|..+|.+-|.++.-+.+.-+||.||-|+.|.+ |+-+=..+-++|+-++.+.
T Consensus 70 gqhlnvnvl~retledav~~pekypqltirvs-----------gyavrfnsltpeqqrdvi~ 120 (127)
T COG3445 70 GQHLNVNVLRRETLEDAVKHPEKYPQLTIRVS-----------GYAVRFNSLTPEQQRDVIA 120 (127)
T ss_pred CceeeeeeeehhhHHHHhhCcccCCceEEEEe-----------eEEEEeccCCHHHhhhHHH
Confidence 45666666666544578889999999988865 4444444455555555443
No 82
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=28.31 E-value=79 Score=21.80 Aligned_cols=20 Identities=15% Similarity=0.386 Sum_probs=14.4
Q ss_pred eEEEeccCCHHHHHHHHHHH
Q 029591 160 KIVITGAKVRDETYTAFENI 179 (191)
Q Consensus 160 kivitGaks~~~~~~a~~~i 179 (191)
+|+|||+++-.|.....+.+
T Consensus 5 rVli~GgR~~~D~~~i~~~L 24 (71)
T PF10686_consen 5 RVLITGGRDWTDHELIWAAL 24 (71)
T ss_pred EEEEEECCccccHHHHHHHH
Confidence 68999999987665544433
No 83
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=27.62 E-value=1.4e+02 Score=19.64 Aligned_cols=28 Identities=11% Similarity=0.103 Sum_probs=19.4
Q ss_pred ceEEEEecCceEEEeccCCHHHHHHHHHH
Q 029591 59 KTTALIFASGKMVCTGAKSEQQSKLAARK 87 (191)
Q Consensus 59 ~~t~lIf~SGKivitGaks~e~a~~a~~~ 87 (191)
.+.+.|-.+|.+.++| .+.+....|.+.
T Consensus 32 g~~I~i~~~g~v~I~G-~~~~~v~~A~~~ 59 (61)
T cd02393 32 GVKIDIEDDGTVYIAA-SDKEAAEKAKKM 59 (61)
T ss_pred CCEEEeCCCCEEEEEe-CCHHHHHHHHHH
Confidence 4566677789999999 445556655543
No 84
>KOG3946 consensus Glutaminyl cyclase [Posttranslational modification, protein turnover, chaperones]
Probab=27.61 E-value=92 Score=27.90 Aligned_cols=58 Identities=16% Similarity=0.302 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHcCCCCccc-----c----eeEEeEEEEEEcCCccChhHHHHhcCCccccccCCCceeEEEe
Q 029591 82 KLAARKYARIIQKLGFPAKFK-----D----FKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRM 146 (191)
Q Consensus 82 ~~a~~~i~~~l~~~g~~~~~~-----~----~~i~Nivat~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~ 146 (191)
+.+-+-+...|+++|..++.. . ..++|+++|.+-.- +..+---|-|+...||+..|+.
T Consensus 72 ~~vr~~i~~~l~~l~w~ve~~~f~~~tp~g~~~f~nii~tl~~~A-------~r~lVlachydsk~~p~~~~vg 138 (338)
T KOG3946|consen 72 RQVRRFIIQHLRNLGWAVETDAFTDNTPLGTRNFNNLIATLDPNA-------SRYLVLACHYDSKIFPGGMFVG 138 (338)
T ss_pred HHHHHHHHHHHHhcCceeeeccccccCcceeeeeeeEEEecCCCc-------chheeeecccccccCCCcceEe
Confidence 444456777788888765332 2 23889999988442 2222235889999999987653
No 85
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=27.41 E-value=1e+02 Score=23.22 Aligned_cols=28 Identities=14% Similarity=0.265 Sum_probs=23.2
Q ss_pred CceEE--EeccCCHHHHHHHHHHHHHHHHHc
Q 029591 67 SGKMV--CTGAKSEQQSKLAARKYARIIQKL 95 (191)
Q Consensus 67 SGKiv--itGaks~e~a~~a~~~i~~~l~~~ 95 (191)
||.++ ++| .++.|++.|++...+.+++.
T Consensus 71 sG~vi~ii~G-~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 71 AGEVIGILAG-PSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred CccEEEEEeC-CCHHHHHHHHHHHHHHHhcc
Confidence 77777 776 68999999999998888764
No 86
>KOG2360 consensus Proliferation-associated nucleolar protein (NOL1) [Cell cycle control, cell division, chromosome partitioning]
Probab=27.20 E-value=67 Score=29.78 Aligned_cols=81 Identities=16% Similarity=0.247 Sum_probs=57.8
Q ss_pred ecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHH-HHHHHHHHHHHHcCCCCcccceeEEeEEEEEEcCCccCh
Q 029591 43 YNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSK-LAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRL 121 (191)
Q Consensus 43 YePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~-~a~~~i~~~l~~~g~~~~~~~~~i~Nivat~~l~~~i~L 121 (191)
=.|+.|+.+.+=+-+|.|+-..-.++.-.++|+..+++-+ +++..+.-++.++-.. |.+.+ +-+-+|++++-..|=
T Consensus 277 ~~~~~~~~v~~iL~DpscSgSgm~~r~~~~~~~e~~~~~rL~~L~~fq~~~~~hal~--fp~~k-~vvystcs~~reene 353 (413)
T KOG2360|consen 277 ATPEKFRDVTYILVDPSCSGSGMVSRQDEDPGAETESPERLENLQSFQIRILKHALT--FPNLK-RLVYSTCSLHREENE 353 (413)
T ss_pred CCcccccceeEEEeCCCCCCCccccceeeccCCCcccHHHHHHHHHHHHHHHHHHhc--CCchh-heeeecchhhhhhhh
Confidence 5678899999999999999999999999999988877666 3444454444443222 33333 234599999988886
Q ss_pred hHHHH
Q 029591 122 EGLAY 126 (191)
Q Consensus 122 ~~la~ 126 (191)
...+.
T Consensus 354 ~vv~d 358 (413)
T KOG2360|consen 354 QVVQE 358 (413)
T ss_pred HHHHH
Confidence 55553
No 87
>COG4274 Uncharacterized conserved protein [Function unknown]
Probab=27.00 E-value=76 Score=23.90 Aligned_cols=60 Identities=12% Similarity=0.115 Sum_probs=46.4
Q ss_pred EEEeccCCHHHHHHHHHHHHHHHHHcCCCCccc--ceeEEeEEEEEEcCCccChhHHHHhcC
Q 029591 70 MVCTGAKSEQQSKLAARKYARIIQKLGFPAKFK--DFKIQNIVGSCDVKFPIRLEGLAYSHG 129 (191)
Q Consensus 70 ivitGaks~e~a~~a~~~i~~~l~~~g~~~~~~--~~~i~Nivat~~l~~~i~L~~la~~~~ 129 (191)
..-.|+|+..|.-+-++.+.+.+++.|.+++.. .+-...+|+.+..+-+..+..++..++
T Consensus 17 ~Td~Gaktlke~p~R~~av~~~les~G~k~~~~y~T~GeYD~V~i~EapDda~~~~~~l~l~ 78 (104)
T COG4274 17 FTDQGAKTLKETPKRAAAVRALLESMGGKVKEQYWTLGEYDVVAIVEAPDDAVATRFSLALA 78 (104)
T ss_pred ccHhHHHHHhhCHHHHHHHHHHHHHcCcEEEEEEEeeccccEEEEEecCCHHHHHHHHHHHH
Confidence 455789999888888888888899999986432 556677888888888888877776543
No 88
>PF11399 DUF3192: Protein of unknown function (DUF3192); InterPro: IPR021534 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=26.99 E-value=1.1e+02 Score=22.89 Aligned_cols=21 Identities=29% Similarity=0.374 Sum_probs=17.5
Q ss_pred CeEEEEEeecceEEEeccCCH
Q 029591 149 PKIVLLIFVSGKIVITGAKVR 169 (191)
Q Consensus 149 ~~~t~lIF~sGkivitGaks~ 169 (191)
-.||-+||.+||++--|-+..
T Consensus 79 DECTplvF~n~~LvgWG~~ay 99 (102)
T PF11399_consen 79 DECTPLVFKNGKLVGWGDDAY 99 (102)
T ss_pred CceEEEEEECCEEEEEcHHhh
Confidence 469999999999999886543
No 89
>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]
Probab=26.47 E-value=43 Score=30.04 Aligned_cols=63 Identities=14% Similarity=0.116 Sum_probs=36.2
Q ss_pred EEEEecCceEEEeccCCHHHHHHHHHHHHHHHHHcCCCCcccceeEEeEEEEEE---cC-CccChhHHHHhc
Q 029591 61 TALIFASGKMVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCD---VK-FPIRLEGLAYSH 128 (191)
Q Consensus 61 t~lIf~SGKivitGaks~e~a~~a~~~i~~~l~~~g~~~~~~~~~i~Nivat~~---l~-~~i~L~~la~~~ 128 (191)
.+.|-+.+.+.+.| -|.+++.. +.+.|++.|+++--..-.+.||+|.-- +. --+|-..|++.+
T Consensus 61 ~i~iT~rqg~ei~~-i~~e~~~~----v~~~L~~iG~~~G~~G~~vr~i~aC~G~~~C~~a~~Dt~~la~~l 127 (317)
T COG2221 61 LIHITSRQGLEIPG-ISPEDADD----VVEELREIGLPVGSTGPAVRAIVACPGPRTCETALYDTTELARRL 127 (317)
T ss_pred eEEEEecCceEecc-CCHHHHHH----HHHHHHHcCCCCCCcchhhhhhhcCcCcccccccccChHHHHHHH
Confidence 34444444444444 45556555 445567999987666667788885422 11 235666666543
No 90
>PF13575 DUF4135: Domain of unknown function (DUF4135)
Probab=26.04 E-value=59 Score=29.06 Aligned_cols=54 Identities=20% Similarity=0.213 Sum_probs=39.7
Q ss_pred EEEeccCCHHHHHHHHHHHHHHHHH---cCCCCcccceeEEeEEEEEEcCCccChhHHHHh
Q 029591 70 MVCTGAKSEQQSKLAARKYARIIQK---LGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYS 127 (191)
Q Consensus 70 ivitGaks~e~a~~a~~~i~~~l~~---~g~~~~~~~~~i~Nivat~~l~~~i~L~~la~~ 127 (191)
|--..+.+.++++.-..++-..|.= +|. .|+--.||+|+.+.|+.||||-|-..
T Consensus 122 I~~~~c~~~~ev~~yY~r~G~llal~y~L~~----~DlH~ENIIa~g~~PvlIDlETlf~~ 178 (370)
T PF13575_consen 122 IEHEPCNSEEEVERYYYRLGVLLALLYLLNG----TDLHFENIIASGEYPVLIDLETLFHP 178 (370)
T ss_pred ecCCCCCCHHHHHHHHHHHHHHHHHHHHhCC----CcccccceEEeCCCcEEEehhhhCCc
Confidence 4445677888888777776555432 343 36677899999999999999998753
No 91
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=25.53 E-value=2.4e+02 Score=19.65 Aligned_cols=52 Identities=15% Similarity=0.264 Sum_probs=30.3
Q ss_pred CCceEEEEecCCce-EEE-Ee-cCce-----EEEeccCCHHHHHHHHHHHHHHHHHcCCCC
Q 029591 47 RFAAVIMRIREPKT-TAL-IF-ASGK-----MVCTGAKSEQQSKLAARKYARIIQKLGFPA 99 (191)
Q Consensus 47 ~fpglv~R~~~P~~-t~l-If-~SGK-----ivitGaks~e~a~~a~~~i~~~l~~~g~~~ 99 (191)
..+||.+|+..... +.. -| .+|| |-..+.-|.++|+..+.++...+++ |.++
T Consensus 21 ~~~GL~l~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~~~-G~dP 80 (89)
T PF13356_consen 21 GVPGLYLRVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALVRQ-GIDP 80 (89)
T ss_dssp ESTTEEEEE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHHCT-T--G
T ss_pred CCCCcEEEEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHHHc-CCCH
Confidence 35899999885522 211 12 3566 3334567889999988888777664 7765
No 92
>cd03005 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.
Probab=25.47 E-value=81 Score=21.65 Aligned_cols=22 Identities=32% Similarity=0.475 Sum_probs=14.7
Q ss_pred EEEeecceEE--EeccCCHHHHHH
Q 029591 153 LLIFVSGKIV--ITGAKVRDETYT 174 (191)
Q Consensus 153 ~lIF~sGkiv--itGaks~~~~~~ 174 (191)
+.+|..|+.+ ..|.++.+++.+
T Consensus 77 ~~~~~~g~~~~~~~G~~~~~~l~~ 100 (102)
T cd03005 77 LLLFKDGEKVDKYKGTRDLDSLKE 100 (102)
T ss_pred EEEEeCCCeeeEeeCCCCHHHHHh
Confidence 4555667654 789998876653
No 93
>PRK10719 eutA reactivating factor for ethanolamine ammonia lyase; Provisional
Probab=25.30 E-value=2.7e+02 Score=26.50 Aligned_cols=30 Identities=17% Similarity=0.217 Sum_probs=24.2
Q ss_pred CCCceeE-EEecCCeEEEEEeecceEEEecc
Q 029591 137 ELFPGLI-YRMKQPKIVLLIFVSGKIVITGA 166 (191)
Q Consensus 137 e~fpgli-~r~~~~~~t~lIF~sGkivitGa 166 (191)
|.-.|+. .-+-.-...+.||..|+++-|++
T Consensus 143 Eke~gVa~IDIGgGTT~iaVf~~G~l~~T~~ 173 (475)
T PRK10719 143 ERNTRVLNIDIGGGTANYALFDAGKVIDTAC 173 (475)
T ss_pred hccCceEEEEeCCCceEEEEEECCEEEEEEE
Confidence 6666775 66777778999999999998875
No 94
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=25.22 E-value=1e+02 Score=26.35 Aligned_cols=32 Identities=22% Similarity=0.404 Sum_probs=26.2
Q ss_pred CeEEEEEeecceEEEeccCCHHHHHHHHHHHHH
Q 029591 149 PKIVLLIFVSGKIVITGAKVRDETYTAFENIYP 181 (191)
Q Consensus 149 ~~~t~lIF~sGkivitGaks~~~~~~a~~~i~~ 181 (191)
+.+=++|| .||+.|.|+-+++.+..|++.+..
T Consensus 183 ~gVP~fv~-d~~~~V~Gaq~~~v~~~al~~~~~ 214 (225)
T COG2761 183 RGVPTFVF-DGKYAVSGAQPYDVLEDALRQLLA 214 (225)
T ss_pred ccCceEEE-cCcEeecCCCCHHHHHHHHHHHHh
Confidence 34446777 999999999999999999887653
No 95
>COG0678 AHP1 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=24.52 E-value=41 Score=27.28 Aligned_cols=32 Identities=13% Similarity=0.223 Sum_probs=25.6
Q ss_pred ccCCCceeEEEec---------CCeEEEEEeecceEEEecc
Q 029591 135 EPELFPGLIYRMK---------QPKIVLLIFVSGKIVITGA 166 (191)
Q Consensus 135 ePe~fpgli~r~~---------~~~~t~lIF~sGkivitGa 166 (191)
..+.+|.++||.+ ....+-.+|...||+++|.
T Consensus 5 vg~klP~vtf~tr~~~~~~~~~~~~ts~~lf~gKkVvlf~l 45 (165)
T COG0678 5 VGKKLPAVTFKTRVGDETADGWVDVTTDDLFKGKKVVLFSL 45 (165)
T ss_pred cCCcCCceEeEEeeccccCCCcccccHHHhcCCCEEEEEeC
Confidence 4577899999876 3456788999999999874
No 96
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=24.32 E-value=1.8e+02 Score=19.98 Aligned_cols=39 Identities=15% Similarity=0.059 Sum_probs=29.8
Q ss_pred EEEEEeecceEEEeccCCHHHHHHHHHHHHHHHHhhhcc
Q 029591 151 IVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 189 (191)
Q Consensus 151 ~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L~~~r~~ 189 (191)
+++.|+..-.-+-.+..+++.++++.+.|-..+.++++.
T Consensus 2 V~v~I~G~~y~i~~~~~~ee~l~~~a~~i~~~i~~~~~~ 40 (89)
T PF05164_consen 2 VKVTILGREYRIKCPDEDEEYLRKAAELINEKINEIKKK 40 (89)
T ss_dssp EEEEETTEEEEECETGCGHHHHHHHHHHHHHHHHHHCTT
T ss_pred eEEEECCEEEEeecCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 445555554444447889999999999999999998865
No 97
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=24.21 E-value=1.3e+02 Score=25.60 Aligned_cols=49 Identities=29% Similarity=0.408 Sum_probs=37.9
Q ss_pred cCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHHHHHcCCCCcccceeEE
Q 029591 56 REPKTTALIFASGKMVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQ 107 (191)
Q Consensus 56 ~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l~~~g~~~~~~~~~i~ 107 (191)
.+.-++++|=.||.|-- +..+-|..++.-+++-|.+.|++++...|+..
T Consensus 11 ~d~~VtlLID~SGSMrg---r~~~vA~~~adila~aL~~~gvp~EVlGFtT~ 59 (219)
T PF11775_consen 11 RDTVVTLLIDCSGSMRG---RPIEVAALCADILARALERCGVPVEVLGFTTR 59 (219)
T ss_pred CCeEEEEEEeCCcCCCC---ChHHHHHHHHHHHHHHHHhCCCCeEEEeeecC
Confidence 34557999999999853 44566777788999999999999776666644
No 98
>cd07996 WGR_MMR_like WGR domain of molybdate metabolism regulator and related proteins. The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.
Probab=24.02 E-value=1.9e+02 Score=19.36 Aligned_cols=33 Identities=27% Similarity=0.263 Sum_probs=25.4
Q ss_pred cCceEEEeccCCHHHHHHHHHHHHHHHHHcCCC
Q 029591 66 ASGKMVCTGAKSEQQSKLAARKYARIIQKLGFP 98 (191)
Q Consensus 66 ~SGKivitGaks~e~a~~a~~~i~~~l~~~g~~ 98 (191)
+.|........|.++|..+++++.+.-.+-|+.
T Consensus 40 ~~Gq~~~~~~~s~~~A~~~~~k~~~~K~~~GY~ 72 (74)
T cd07996 40 TKGQSRTKTFDSEEEALKAAEKLIREKLKRGYR 72 (74)
T ss_pred CCCceEEEECCCHHHHHHHHHHHHHHHHhcCCC
Confidence 356666777788999999999988776666764
No 99
>COG4810 EutS Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=23.91 E-value=1.3e+02 Score=22.75 Aligned_cols=28 Identities=25% Similarity=0.256 Sum_probs=24.0
Q ss_pred cCceEEEeccCCHHHHHHHHHHHHHHHHHc
Q 029591 66 ASGKMVCTGAKSEQQSKLAARKYARIIQKL 95 (191)
Q Consensus 66 ~SGKivitGaks~e~a~~a~~~i~~~l~~~ 95 (191)
-||-++.|| +....+.|++.+.+-|.++
T Consensus 83 FsGalvltG--dv~aVE~aLkqv~~~L~e~ 110 (121)
T COG4810 83 FSGALVLTG--DVGAVEEALKQVVSGLGEL 110 (121)
T ss_pred ccceEEEEc--chHHHHHHHHHHHHHHHHH
Confidence 489999999 6788899999998888774
No 100
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=23.83 E-value=1.3e+02 Score=18.55 Aligned_cols=25 Identities=16% Similarity=0.193 Sum_probs=20.0
Q ss_pred EEEeccCCHHHHHHHHHHHHHHHHH
Q 029591 70 MVCTGAKSEQQSKLAARKYARIIQK 94 (191)
Q Consensus 70 ivitGaks~e~a~~a~~~i~~~l~~ 94 (191)
+.-.|.++..||..+..++...+++
T Consensus 19 ~~k~GF~TkkeA~~~~~~~~~~~~~ 43 (46)
T PF14657_consen 19 KTKRGFKTKKEAEKALAKIEAELEN 43 (46)
T ss_pred EEcCCCCcHHHHHHHHHHHHHHHHc
Confidence 4557899999999999998766543
No 101
>cd02988 Phd_like_VIAF Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=23.65 E-value=54 Score=26.83 Aligned_cols=35 Identities=14% Similarity=0.253 Sum_probs=21.0
Q ss_pred eEEEEecCceEE--EeccCCHHHHHHHHHHHHHHHHH
Q 029591 60 TTALIFASGKMV--CTGAKSEQQSKLAARKYARIIQK 94 (191)
Q Consensus 60 ~t~lIf~SGKiv--itGaks~e~a~~a~~~i~~~l~~ 94 (191)
.|+++|.+|+++ +.|+.....-.-..+.+-..|.+
T Consensus 154 PTlliyk~G~~v~~ivG~~~~gg~~~~~~~lE~~L~~ 190 (192)
T cd02988 154 PTILVYRNGDIVKQFIGLLEFGGMNTTMEDLEWLLVQ 190 (192)
T ss_pred CEEEEEECCEEEEEEeCchhhCCCCCCHHHHHHHHHh
Confidence 399999999998 66765443223333344444443
No 102
>TIGR01651 CobT cobaltochelatase, CobT subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=23.62 E-value=1.2e+02 Score=29.57 Aligned_cols=46 Identities=26% Similarity=0.335 Sum_probs=35.7
Q ss_pred ceEEEEecCceEEEeccCCHHHHHHHHHHHHHHHHHcCCCCcccceeEE
Q 029591 59 KTTALIFASGKMVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQ 107 (191)
Q Consensus 59 ~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l~~~g~~~~~~~~~i~ 107 (191)
.++++|=.||.|. | +..+-|..++.-+.+-|+++|+++.+..|+..
T Consensus 394 ~V~LLID~SGSM~--~-r~~~vA~~~a~iLa~aL~~~gIp~eVlGFtt~ 439 (600)
T TIGR01651 394 VVTLLIDNSGSMR--G-RPITVAATCADILARTLERCGVKVEILGFTTR 439 (600)
T ss_pred EEEEEEECCccCC--C-CHHHHHHHHHHHHHHHHHHCCCCeEEEeeccc
Confidence 3688999999995 4 44555667788999999999999777666643
No 103
>CHL00041 rps11 ribosomal protein S11
Probab=23.33 E-value=3.1e+02 Score=20.69 Aligned_cols=51 Identities=18% Similarity=0.258 Sum_probs=34.3
Q ss_pred CceEEEEecCCce-EEEEecCceEEEeccC--CHHHHHHHHHHHHHHHHHcCCC
Q 029591 48 FAAVIMRIREPKT-TALIFASGKMVCTGAK--SEQQSKLAARKYARIIQKLGFP 98 (191)
Q Consensus 48 fpglv~R~~~P~~-t~lIf~SGKivitGak--s~e~a~~a~~~i~~~l~~~g~~ 98 (191)
|+-.++-+.|++- ++...++|.+--.|++ +.-.+..+++++.+.+.++|+.
T Consensus 22 ~NNTiiTlTd~~G~~l~~~S~G~~gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~ 75 (116)
T CHL00041 22 FNNTIVTVTDVRGRVISWSSAGACGFKGARKGTPFAAQTAAENAIRTVIDQGMK 75 (116)
T ss_pred cCCEEEEEEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 3444555555554 3444566888777765 3447888888898998888875
No 104
>PRK09929 hypothetical protein; Provisional
Probab=23.28 E-value=91 Score=22.92 Aligned_cols=23 Identities=9% Similarity=0.044 Sum_probs=19.0
Q ss_pred cceEEEeccCCHHHHHHHHHHHH
Q 029591 158 SGKIVITGAKVRDETYTAFENIY 180 (191)
Q Consensus 158 sGkivitGaks~~~~~~a~~~i~ 180 (191)
-|-|.++|..+++|+++++..-.
T Consensus 40 iGtVSvs~~~s~~d~~~~La~KA 62 (91)
T PRK09929 40 IGTISTSNEMSTADAKEDLIKKA 62 (91)
T ss_pred eEEEEEcCCCCHHHHHHHHHHHH
Confidence 48889999999999999887543
No 105
>COG4978 Transcriptional regulator, effector-binding domain/component [Transcription / Signal transduction mechanisms]
Probab=22.79 E-value=1.6e+02 Score=23.36 Aligned_cols=43 Identities=19% Similarity=0.271 Sum_probs=35.8
Q ss_pred CCceEEEEecCceEEEeccC-CHHHHHHHHHHHHHHHHHcCCCC
Q 029591 57 EPKTTALIFASGKMVCTGAK-SEQQSKLAARKYARIIQKLGFPA 99 (191)
Q Consensus 57 ~P~~t~lIf~SGKivitGak-s~e~a~~a~~~i~~~l~~~g~~~ 99 (191)
++......+.+||+.++=-+ +-++...+.+++..-+++.|.++
T Consensus 79 ~~~~~~~~~P~g~~a~~~~~G~~~~~~~~y~rli~~iee~g~~i 122 (153)
T COG4978 79 DIDIKIKTLPKGKYACIIHKGSYEEVEQAYKRLIEYIEENGLEI 122 (153)
T ss_pred CCcceeEEccCceEEEEEEEcCcccHHHHHHHHHHHHHHhCCcc
Confidence 46678888889977776555 88999999999999999998865
No 106
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=22.53 E-value=3.3e+02 Score=20.22 Aligned_cols=51 Identities=25% Similarity=0.480 Sum_probs=34.1
Q ss_pred CceEEEEecCCceEEEEe-cCceEEEeccC--CHHHHHHHHHHHHHHHHHcCCC
Q 029591 48 FAAVIMRIREPKTTALIF-ASGKMVCTGAK--SEQQSKLAARKYARIIQKLGFP 98 (191)
Q Consensus 48 fpglv~R~~~P~~t~lIf-~SGKivitGak--s~e~a~~a~~~i~~~l~~~g~~ 98 (191)
|+-.++-+.+++-..+.| ++|.+--.|++ +.-.+..+++++.+.++++|+.
T Consensus 9 ~NNT~itlTd~~g~~~~~~S~G~~gfkg~rk~t~~Aa~~~a~~~~~~~~~~gi~ 62 (108)
T TIGR03632 9 FNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFGMK 62 (108)
T ss_pred CCCEEEEEEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 344556666765444444 56777766654 2346888888998999998875
No 107
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=22.10 E-value=1.2e+02 Score=21.29 Aligned_cols=23 Identities=30% Similarity=0.443 Sum_probs=14.2
Q ss_pred EEee-cceEE--EeccCCHHHHHHHH
Q 029591 154 LIFV-SGKIV--ITGAKVRDETYTAF 176 (191)
Q Consensus 154 lIF~-sGkiv--itGaks~~~~~~a~ 176 (191)
.++. .|+++ ++|..+.+++.+.+
T Consensus 87 ~~~d~~G~~v~~~~G~~~~~~l~~~L 112 (112)
T PF13098_consen 87 VFLDKDGKIVYRIPGYLSPEELLKML 112 (112)
T ss_dssp EECTTTSCEEEEEESS--HHHHHHHH
T ss_pred EEEcCCCCEEEEecCCCCHHHHHhhC
Confidence 4443 57744 79999999887653
No 108
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=21.93 E-value=98 Score=19.85 Aligned_cols=20 Identities=40% Similarity=0.519 Sum_probs=16.2
Q ss_pred cceEEEeccCCHHHHHHHHHHH
Q 029591 158 SGKIVITGAKVRDETYTAFENI 179 (191)
Q Consensus 158 sGkivitGaks~~~~~~a~~~i 179 (191)
++.|+|+|. .+.+..|.+.|
T Consensus 42 ~~~v~I~G~--~~~v~~A~~~i 61 (62)
T cd02394 42 SDTITITGP--KENVEKAKEEI 61 (62)
T ss_pred CCEEEEEcC--HHHHHHHHHHh
Confidence 689999999 56788887765
No 109
>cd07047 BMC_PduB_repeat1 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 1. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduB).
Probab=21.67 E-value=1.5e+02 Score=23.27 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=23.9
Q ss_pred CceEEEeccCCHHHHHHHHHHHHHHHHH
Q 029591 67 SGKMVCTGAKSEQQSKLAARKYARIIQK 94 (191)
Q Consensus 67 SGKivitGaks~e~a~~a~~~i~~~l~~ 94 (191)
+|-++++|+.++.+++.|++--.+.+.+
T Consensus 78 kg~vvitGg~dVs~V~~aVeaa~~~v~~ 105 (134)
T cd07047 78 HGSLILFGAEDVSDVRRAVEVALSETEK 105 (134)
T ss_pred eEEEEEEcCCCHHHHHHHHHHHHHHHHH
Confidence 7889999999999988888877777665
No 110
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=21.42 E-value=86 Score=19.99 Aligned_cols=25 Identities=12% Similarity=0.169 Sum_probs=18.4
Q ss_pred EEeecceEEEeccCCH---HHHHHHHHH
Q 029591 154 LIFVSGKIVITGAKVR---DETYTAFEN 178 (191)
Q Consensus 154 lIF~sGkivitGaks~---~~~~~a~~~ 178 (191)
.=|.+|+++|++.... +++.++++.
T Consensus 31 vd~~~~~v~v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 31 VDLETKTVTVTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp EETTTTEEEEEESTTTSCHHHHHHHHHH
T ss_pred EECCCCEEEEEEecCCCCHHHHHHHHHH
Confidence 4577899999998766 667666654
No 111
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=21.00 E-value=99 Score=25.10 Aligned_cols=57 Identities=16% Similarity=0.333 Sum_probs=31.7
Q ss_pred EEEEecCceEEEeccCCHHHHHHHHHHHHHHHHHcC--CCCcccceeEEeEEEEEEcCC-----ccChhHHHH
Q 029591 61 TALIFASGKMVCTGAKSEQQSKLAARKYARIIQKLG--FPAKFKDFKIQNIVGSCDVKF-----PIRLEGLAY 126 (191)
Q Consensus 61 t~lIf~SGKivitGaks~e~a~~a~~~i~~~l~~~g--~~~~~~~~~i~Nivat~~l~~-----~i~L~~la~ 126 (191)
+..-+.|+.+++.| .+.+|...|++++ .++| +-+ ..+ ..+++...||. ....++++.
T Consensus 59 sS~ahDshniiviG-~~~~dm~~A~n~l----~~~gGG~vv-v~~---g~v~a~lpLpi~GlmS~~~~eev~~ 122 (171)
T PF13382_consen 59 SSVAHDSHNIIVIG-TNDEDMALAANRL----IEMGGGIVV-VDD---GEVLAELPLPIAGLMSDLPAEEVAR 122 (171)
T ss_dssp ES--TTT--EEEEE-SSHHHHHHHHHHH----HHTTSEEEE-EET---TEEEEEEE-TBTTTBBSS-HHHHHH
T ss_pred EEcccCCCCEEEEE-CCHHHHHHHHHHH----HHhCCCEEE-EEC---CEEEEEEeccccceecCCCHHHHHH
Confidence 33445699999999 5789999999887 4442 321 111 34677777762 344555554
No 112
>KOG3384 consensus Selenoprotein [General function prediction only]
Probab=20.93 E-value=64 Score=25.70 Aligned_cols=26 Identities=38% Similarity=0.639 Sum_probs=19.2
Q ss_pred ccCCCceeEEE---ecCCeEEEEEeecceE
Q 029591 135 EPELFPGLIYR---MKQPKIVLLIFVSGKI 161 (191)
Q Consensus 135 ePe~fpgli~r---~~~~~~t~lIF~sGki 161 (191)
+|++|||+..+ -.+|.+ .+.=.+||+
T Consensus 101 ~~~kFp~vkvkyVrg~~P~l-~llDadgk~ 129 (154)
T KOG3384|consen 101 EPEKFPGVKVKYVRGSDPVL-KLLDADGKH 129 (154)
T ss_pred chhhCCCceEEEecCCCCee-EeecCCCCc
Confidence 89999999754 345655 577788885
No 113
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=20.89 E-value=2.4e+02 Score=22.09 Aligned_cols=52 Identities=25% Similarity=0.415 Sum_probs=38.8
Q ss_pred CCceEEEEecCCceEEEEe-cCceEEEeccC--CHHHHHHHHHHHHHHHHHcCCC
Q 029591 47 RFAAVIMRIREPKTTALIF-ASGKMVCTGAK--SEQQSKLAARKYARIIQKLGFP 98 (191)
Q Consensus 47 ~fpglv~R~~~P~~t~lIf-~SGKivitGak--s~e~a~~a~~~i~~~l~~~g~~ 98 (191)
-|+-=++-+.|+.-..++| ++|.+..-|.+ +.=.|..|++...+..++.|+.
T Consensus 26 sfNNTivtitD~~Gn~i~wassG~~gfk~~rk~tpyAA~~aa~~aa~~a~e~Gi~ 80 (129)
T COG0100 26 SFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKKAKEHGIK 80 (129)
T ss_pred ccCCcEEEecCCCCCEEEEEecCCceEcCCCCCCHHHHHHHHHHHHHHHHHhCcc
Confidence 4555667777877666666 68999999987 2336778888888888888875
No 114
>PRK05309 30S ribosomal protein S11; Validated
Probab=20.74 E-value=3.5e+02 Score=20.81 Aligned_cols=51 Identities=18% Similarity=0.377 Sum_probs=33.4
Q ss_pred CceEEEEecCCceEEEEe-cCceEEEeccC--CHHHHHHHHHHHHHHHHHcCCC
Q 029591 48 FAAVIMRIREPKTTALIF-ASGKMVCTGAK--SEQQSKLAARKYARIIQKLGFP 98 (191)
Q Consensus 48 fpglv~R~~~P~~t~lIf-~SGKivitGak--s~e~a~~a~~~i~~~l~~~g~~ 98 (191)
|+-.++-+.|+.-..+.| ++|.+-..|++ +...+..+++++.+.+.++|+.
T Consensus 26 ~NNTiitlTd~~G~~~~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~ 79 (128)
T PRK05309 26 FNNTIVTITDRQGNVISWASAGGLGFKGSRKSTPYAAQVAAEDAAKKAKEHGMK 79 (128)
T ss_pred CCCEEEEEEcCCCCEEEEEecCccEeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 344555556655444444 56777666654 3446788888888888888885
No 115
>cd01554 EPT-like Enol pyruvate transferases family includes EPSP synthases and UDP-N-acetylglucosamine enolpyruvyl transferase. Both enzymes catalyze the reaction of enolpyruvyl transfer.
Probab=20.72 E-value=37 Score=30.19 Aligned_cols=32 Identities=13% Similarity=0.302 Sum_probs=24.0
Q ss_pred cCceEEEeccCCHHHHHHHHHHHHHHHHHcCCCCcc
Q 029591 66 ASGKMVCTGAKSEQQSKLAARKYARIIQKLGFPAKF 101 (191)
Q Consensus 66 ~SGKivitGaks~e~a~~a~~~i~~~l~~~g~~~~~ 101 (191)
..|++.+.|..... ....+.+.|+++|.++..
T Consensus 239 ~~~~v~i~~~~~~~----~~~~~~~~L~~~G~~v~~ 270 (408)
T cd01554 239 APGRLVLQNVGINE----TRTGIIDVLRAMGAKIEI 270 (408)
T ss_pred cCCeEEEecCCCCc----hhhHHHHHHHHcCCEEEE
Confidence 45889999976432 667888999999987544
No 116
>cd02975 PfPDO_like_N Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI), which are both involved in oxidative protein folding. PfPDO contains two redox active CXXC motifs in two contiguous TRX-fold subdomains. The active site in the N-terminal TRX-fold subdomain is required for isomerase but not for reductase activity of PfPDO. The exclusive presence of PfPDO-like proteins in extremophiles may suggest that they have a special role in adaptation to extreme conditions.
Probab=20.70 E-value=2.1e+02 Score=20.83 Aligned_cols=30 Identities=20% Similarity=0.200 Sum_probs=23.4
Q ss_pred EEEEeec----ceEEEeccCCHHHHHHHHHHHHH
Q 029591 152 VLLIFVS----GKIVITGAKVRDETYTAFENIYP 181 (191)
Q Consensus 152 t~lIF~s----GkivitGaks~~~~~~a~~~i~~ 181 (191)
++++|.. |++...|..+.+++.+-++.|+.
T Consensus 78 t~~i~~~g~~~~~~~~~G~~~~~el~~~i~~i~~ 111 (113)
T cd02975 78 TTIFLQDGGKDGGIRYYGLPAGYEFASLIEDIVR 111 (113)
T ss_pred EEEEEeCCeecceEEEEecCchHHHHHHHHHHHh
Confidence 5667764 66778999999999988887764
No 117
>cd02950 TxlA TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport.
Probab=20.25 E-value=1.9e+02 Score=22.05 Aligned_cols=28 Identities=11% Similarity=0.100 Sum_probs=20.4
Q ss_pred EEEEe-cCceEE--EeccCCHHHHHHHHHHH
Q 029591 61 TALIF-ASGKMV--CTGAKSEQQSKLAARKY 88 (191)
Q Consensus 61 t~lIf-~SGKiv--itGaks~e~a~~a~~~i 88 (191)
++.+| .+|+++ ..|....++.+..++++
T Consensus 79 t~v~~~~~G~~v~~~~G~~~~~~l~~~l~~l 109 (142)
T cd02950 79 HFVFLDREGNEEGQSIGLQPKQVLAQNLDAL 109 (142)
T ss_pred EEEEECCCCCEEEEEeCCCCHHHHHHHHHHH
Confidence 66777 489988 67988877776655554
No 118
>COG2403 Predicted GTPase [General function prediction only]
Probab=20.17 E-value=5.3e+02 Score=24.17 Aligned_cols=101 Identities=12% Similarity=0.168 Sum_probs=64.3
Q ss_pred EEEEEEcCCccCHHHHHhhC----CCceecCCCCceEEEEecCCceEEEEecCceEEEeccCCHHHHHHHHHHHHHHHHH
Q 029591 19 IVSTVNLDCKLDLKKIALQA----RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAARKYARIIQK 94 (191)
Q Consensus 19 vVas~~l~~~ldL~~la~~~----~n~eYePe~fpglv~R~~~P~~t~lIf~SGKivitGaks~e~a~~a~~~i~~~l~~ 94 (191)
|++-++=+-.++-...+... +-..+.--+|+|..=|+..|+..-..+-+|-=+.++ +|.+ .+-+.|++
T Consensus 9 viiLgaggrdfhv~n~a~r~~~~yevvaf~aaqiiG~~er~yppsleg~~~p~Gvpi~~~-k~~~-------~lek~ire 80 (449)
T COG2403 9 VIILGAGGRDFHVFNVALRDNPEYEVVAFTAAQIIGGTERIYPPSLEGVLYPLGVPILPE-KDYD-------DLEKIIRE 80 (449)
T ss_pred EEEEeccCcccchhhHHhccCCcceEEEEEEEEecCCccccCCCCcccccccCCcccccc-ccHH-------HHHHHHHH
Confidence 55666666666666666542 234566678888888999998888888999888887 5533 33444777
Q ss_pred cCCCCcccceeEEeEEEEEEcCCccChhHHHHhcCCccccc
Q 029591 95 LGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYE 135 (191)
Q Consensus 95 ~g~~~~~~~~~i~Nivat~~l~~~i~L~~la~~~~~~~~Ye 135 (191)
.+.+ .-+.+-.|+...-...-.+..++..+.|-
T Consensus 81 ~~VD--------~~VlaySDvs~e~v~~IaS~vLs~GA~f~ 113 (449)
T COG2403 81 KDVD--------IVVLAYSDVSYEHVFRIASRVLSAGADFK 113 (449)
T ss_pred cCCC--------eEEEEcccCCHHHHHHHHHHHHhCCceeE
Confidence 7665 23556667555444444444555445554
No 119
>PF03332 PMM: Eukaryotic phosphomannomutase; InterPro: IPR005002 This enzyme (5.4.2.8 from EC) is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions.; GO: 0004615 phosphomannomutase activity, 0019307 mannose biosynthetic process, 0005737 cytoplasm; PDB: 2I55_B 2I54_C 3F9R_A 2FUE_A 2FUC_A 2AMY_A 2Q4R_A.
Probab=20.15 E-value=1.5e+02 Score=25.27 Aligned_cols=91 Identities=19% Similarity=0.367 Sum_probs=46.4
Q ss_pred EEecCceEEEe----ccCCHHHHHHHHHHHHHHHHHcCCCCcc---cceeEEeEEEEEEcCCccChhHHHHhcCCccccc
Q 029591 63 LIFASGKMVCT----GAKSEQQSKLAARKYARIIQKLGFPAKF---KDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYE 135 (191)
Q Consensus 63 lIf~SGKivit----Gaks~e~a~~a~~~i~~~l~~~g~~~~~---~~~~i~Nivat~~l~~~i~L~~la~~~~~~~~Ye 135 (191)
..|+.|+.... -.-++|..+..++-+.+.+.+++++++. .+++ .-++.-+-+|..=.+++=. .+.+|+
T Consensus 48 ~~y~~~~~~~~~~~~~~lgee~~~~~in~~l~~~~~l~lp~krGtfIE~R-~gmIn~SpiGr~a~~eer~----~f~~~D 122 (220)
T PF03332_consen 48 VAYKNGELIWSQSIAEFLGEEKLQKLINFCLRYISDLDLPVKRGTFIEFR-GGMINFSPIGRNASQEERD----EFDEYD 122 (220)
T ss_dssp EEEETTEEEEE--HHHHHHHHHHHHHHHHHHHHHHT---S---S-SEEEE-SSEEEE-SS-TTS-HHHHH----HHHHHH
T ss_pred eEEECCCchhhHhHHHHcCHHHHHHHHHHHHHHHHhCCCCccCCCceeec-CCcEEECcccCcCCHHHHH----hhhhcC
Confidence 35566655542 3345677888888888889999987643 3344 2233333345433333211 122333
Q ss_pred -------------cCCCce--eEEEecCCeEEEEEeecc
Q 029591 136 -------------PELFPG--LIYRMKQPKIVLLIFVSG 159 (191)
Q Consensus 136 -------------Pe~fpg--li~r~~~~~~t~lIF~sG 159 (191)
.+.||. |.|++-+. +++-||+.|
T Consensus 123 ~~~~iR~~~v~~L~~~f~d~~L~~siGGq-iSiDvfp~G 160 (220)
T PF03332_consen 123 KKHKIREKLVEALKKEFPDFGLTFSIGGQ-ISIDVFPKG 160 (220)
T ss_dssp HHHTHHHHHHHHHHHHTCCCSEEEEEETT-TEEEEEETT
T ss_pred hhhhHHHHHHHHHHHHCCCCceEEecCCc-eEEccccCC
Confidence 345884 88998654 566777766
No 120
>PF05906 DUF865: Herpesvirus-7 repeat of unknown function (DUF865)
Probab=20.14 E-value=1.2e+02 Score=17.95 Aligned_cols=25 Identities=16% Similarity=0.354 Sum_probs=19.4
Q ss_pred ccCCCceeEEEecCCeEEEEEeecc
Q 029591 135 EPELFPGLIYRMKQPKIVLLIFVSG 159 (191)
Q Consensus 135 ePe~fpgli~r~~~~~~t~lIF~sG 159 (191)
.|.-+.-|.|+..+..-+..||+-|
T Consensus 10 rpqphnpltfkpvkttgtavvfsag 34 (35)
T PF05906_consen 10 RPQPHNPLTFKPVKTTGTAVVFSAG 34 (35)
T ss_pred CCCCCCccceeeeeccceEEEeecc
Confidence 4555667888888877888999887
No 121
>PF08622 Svf1: Svf1-like; InterPro: IPR013931 This entry represents oxidative stress survival proteins, such as Svf1. The protein Svf1 is required for yeast survival under conditions of oxidative stress, including cold stress []. Cells deficient in Svf1 have increased levels of reactive oxygen species (ROS) under certain conditions. ; GO: 0006979 response to oxidative stress
Probab=20.10 E-value=2.2e+02 Score=25.67 Aligned_cols=47 Identities=21% Similarity=0.398 Sum_probs=35.7
Q ss_pred HHHHHhhCCCceecCCCCceEEEEecCCc----eEEEE---ecCceEEEeccCC
Q 029591 31 LKKIALQARNAEYNPKRFAAVIMRIREPK----TTALI---FASGKMVCTGAKS 77 (191)
Q Consensus 31 L~~la~~~~n~eYePe~fpglv~R~~~P~----~t~lI---f~SGKivitGaks 77 (191)
...+|....-+-|.-+.+.++.|.+..|+ .++.| -..|||++.|+.+
T Consensus 168 PhhaA~~WNF~~Fqs~~~Sav~MEFTTp~sYg~t~V~vg~i~~~~kii~v~~~n 221 (325)
T PF08622_consen 168 PHHAASRWNFLNFQSPTYSAVMMEFTTPPSYGSTTVNVGSIVKDGKIIAVGSDN 221 (325)
T ss_pred cchhhhcceeEEecCCCeEEEEEEEecCcccCCeEEEEEEEEeCCEEEEEecCc
Confidence 35566665558899999999999998885 34444 4699999999843
Done!